Discussion:
principal component analysis
(too old to reply)
yoshizawa006
2006-04-02 13:13:38 UTC
Permalink
Hello,

I would like to use PCA analysis in the dihedral space.

Despite having read the topics related to this issue in the GROMACS page I am not quite sure how to accomplish this :-)

The -or option in the g_angle (version 3.3) seems not to be working. I am already using an index file as sugested in the archives.

Best wishes

Maki Yoshizawa







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David van der Spoel
2006-04-02 17:30:40 UTC
Permalink
Post by yoshizawa006
Hello,
I would like to use PCA analysis in the dihedral space.
Despite having read the topics related to this issue in the GROMACS page
I am not quite sure how to accomplish this :-)
The -or option in the g_angle (version 3.3) seems not to be working. I
am already using an index file as sugested in the archives.
more info please.
did you use -type dihedral ?
Post by yoshizawa006
Best wishes
Maki Yoshizawa
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--
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________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
yoshizawa006
2006-04-03 00:04:21 UTC
Permalink
Dear David,
thank you very much for your reply!
Indeed I have used -type dihedral.
Could it be, the problem lies in the [].tpr and [].xtc files? I mean, which subset of atoms must I choose in those files? (This very part of the previous discussion was obscure to me!)
Best wishes!
Maki Yoshizawa
Post by yoshizawa006
Hello,
I would like to use PCA analysis in the dihedral space.
Despite having read the topics related to this issue in the GROMACS page
I am not quite sure how to accomplish this :-)
The -or option in the g_angle (version 3.3) seems not to be working. I
am already using an index file as sugested in the archives.
more info please.
did you use -type dihedral ?
Post by yoshizawa006
Best wishes
Maki Yoshizawa
------------------------------------------------------------------------
Celebrate Yahoo! JAPAN 10th Anniversary
------------------------------------------------------------------------
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
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www interface or send it to gmx-users-request at gromacs.org.
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
_______________________________________________
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raja
2006-04-03 07:00:37 UTC
Permalink
Dear gmxions,
I tried to compile gromacs in SGI IRIX6.5. I followed configuring and
installing of fftw, both single and double precision as per gromacs
website. When I tried to configure gromacs...it says.." Cannot find any
single precision fftw.h or sfftw.h". I also checked the
"/usr/local/include/". The folder contains 2 files "fftw3.f" and
"fftw3.h". More I had the experince of compiling under cygwin. So I did
crosscheck for files under folder in cygwin (/usr/local/include/ )
found exactly same files there too as "fftw3.f" and "fftw3.h". But the
configuration of gromacs worked in cygwin without any error, otherhand
why it fails in SGI ? Please help me out !

I also pasted detailed error output while configuring gromacs in SGI.
###############################################################################
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... no
checking dynamic linker characteristics... irix6.5 ld.so
checking whether ln -s works... yes
checking for sqrt in -lm... yes
checking for fftw.h... no
checking for sfftw.h... no
configure: error: Cannot find any single precision fftw.h or sfftw.h
Do you have single precision FFTW installed? If you are using packages,
note that you also need fftw-devel to compile GROMACS. You can find the
software at www.fftw.org, and detailed instructions at www.gromacs.org.
If you compiled FFTW yourself:
Note that the default FFTW setup is double precision. Change the FFTW
configuration to single with --enable-float. If you want MPI support,
use --enable-mpi. It is a good idea to install both single & double.
If your sysadm doesn't want to install it you can do it to a location
in your home directory and provide the correct paths in ......
###################################################################################

With thanks !
B.Nataraj
--
raja
raja_28 at fastmail.us
--
http://www.fastmail.fm - Same, same, but different
David van der Spoel
2006-04-03 07:06:22 UTC
Permalink
Post by raja
Dear gmxions,
I tried to compile gromacs in SGI IRIX6.5. I followed configuring and
installing of fftw, both single and double precision as per gromacs
website. When I tried to configure gromacs...it says.." Cannot find any
single precision fftw.h or sfftw.h". I also checked the
"/usr/local/include/". The folder contains 2 files "fftw3.f" and
"fftw3.h". More I had the experince of compiling under cygwin. So I did
crosscheck for files under folder in cygwin (/usr/local/include/ )
found exactly same files there too as "fftw3.f" and "fftw3.h". But the
configuration of gromacs worked in cygwin without any error, otherhand
why it fails in SGI ? Please help me out !
Maybe you explicitly have to add /usr/local/include to the CPPFLAGS
environment variable.

Do you have the corresponding libraries in /usr/local/lib?
Post by raja
I also pasted detailed error output while configuring gromacs in SGI.
###############################################################################
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... no
checking dynamic linker characteristics... irix6.5 ld.so
checking whether ln -s works... yes
checking for sqrt in -lm... yes
checking for fftw.h... no
checking for sfftw.h... no
configure: error: Cannot find any single precision fftw.h or sfftw.h
Do you have single precision FFTW installed? If you are using packages,
note that you also need fftw-devel to compile GROMACS. You can find the
software at www.fftw.org, and detailed instructions at www.gromacs.org.
Note that the default FFTW setup is double precision. Change the FFTW
configuration to single with --enable-float. If you want MPI support,
use --enable-mpi. It is a good idea to install both single & double.
If your sysadm doesn't want to install it you can do it to a location
in your home directory and provide the correct paths in ......
###################################################################################
With thanks !
B.Nataraj
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
raja
2006-04-03 07:44:37 UTC
Permalink
Dear Mr.Spoel,
Thanks for your reply. Yea I checked , the corresponding files are
there is "/usr/local/lib". Totally 8 files and
1 folder called "pkgconfig". More I also tried to set envirnomental
variable to CPPFLAGS and LDFLAGS as command before configure but no
effect.
May I have to add these environmental variables in my .cshrc file ?.

Please suggest me any other flags to be enabled or disabled to make
configure to get path of fftw library files.

With thanks!
B.Nataraj

On Mon, 03 Apr 2006 09:06:22 +0200, "David van der Spoel"
Post by David van der Spoel
Post by raja
Dear gmxions,
I tried to compile gromacs in SGI IRIX6.5. I followed configuring and
installing of fftw, both single and double precision as per gromacs
website. When I tried to configure gromacs...it says.." Cannot find any
single precision fftw.h or sfftw.h". I also checked the
"/usr/local/include/". The folder contains 2 files "fftw3.f" and
"fftw3.h". More I had the experince of compiling under cygwin. So I did
crosscheck for files under folder in cygwin (/usr/local/include/ )
found exactly same files there too as "fftw3.f" and "fftw3.h". But the
configuration of gromacs worked in cygwin without any error, otherhand
why it fails in SGI ? Please help me out !
Maybe you explicitly have to add /usr/local/include to the CPPFLAGS
environment variable.
Do you have the corresponding libraries in /usr/local/lib?
Post by raja
I also pasted detailed error output while configuring gromacs in SGI.
###############################################################################
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... no
checking dynamic linker characteristics... irix6.5 ld.so
checking whether ln -s works... yes
checking for sqrt in -lm... yes
checking for fftw.h... no
checking for sfftw.h... no
configure: error: Cannot find any single precision fftw.h or sfftw.h
Do you have single precision FFTW installed? If you are using packages,
note that you also need fftw-devel to compile GROMACS. You can find the
software at www.fftw.org, and detailed instructions at www.gromacs.org.
Note that the default FFTW setup is double precision. Change the FFTW
configuration to single with --enable-float. If you want MPI support,
use --enable-mpi. It is a good idea to install both single & double.
If your sysadm doesn't want to install it you can do it to a location
in your home directory and provide the correct paths in ......
###################################################################################
With thanks !
B.Nataraj
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
raja
raja_28 at fastmail.us
--
http://www.fastmail.fm - A fast, anti-spam email service.
Erik Lindahl
2006-04-03 08:05:53 UTC
Permalink
Hi,

Please read through and follow the detailed installation instructions at

http://www.gromacs.org/installation/index.php

Based in the limited output below it looks as if you are either
trying to install an earlier version of Gromacs without support for
FFTW-3, or you have manually selected FFTW-2.

Cheers,

Erik
Post by raja
Dear Mr.Spoel,
Thanks for your reply. Yea I checked , the corresponding files are
there is "/usr/local/lib". Totally 8 files and
1 folder called "pkgconfig". More I also tried to set envirnomental
variable to CPPFLAGS and LDFLAGS as command before configure but no
effect.
May I have to add these environmental variables in my .cshrc file ?.
Please suggest me any other flags to be enabled or disabled to make
configure to get path of fftw library files.
With thanks!
B.Nataraj
On Mon, 03 Apr 2006 09:06:22 +0200, "David van der Spoel"
Post by David van der Spoel
Post by raja
Dear gmxions,
I tried to compile gromacs in SGI IRIX6.5. I followed configuring and
installing of fftw, both single and double precision as per gromacs
website. When I tried to configure gromacs...it says.." Cannot find any
single precision fftw.h or sfftw.h". I also checked the
"/usr/local/include/". The folder contains 2 files "fftw3.f" and
"fftw3.h". More I had the experince of compiling under cygwin. So I did
crosscheck for files under folder in cygwin (/usr/local/include/ )
found exactly same files there too as "fftw3.f" and "fftw3.h". But the
configuration of gromacs worked in cygwin without any error,
otherhand
why it fails in SGI ? Please help me out !
Maybe you explicitly have to add /usr/local/include to the CPPFLAGS
environment variable.
Do you have the corresponding libraries in /usr/local/lib?
Post by raja
I also pasted detailed error output while configuring gromacs in SGI.
####################################################################
###########
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... no
checking dynamic linker characteristics... irix6.5 ld.so
checking whether ln -s works... yes
checking for sqrt in -lm... yes
checking for fftw.h... no
checking for sfftw.h... no
configure: error: Cannot find any single precision fftw.h or sfftw.h
Do you have single precision FFTW installed? If you are using packages,
note that you also need fftw-devel to compile GROMACS. You can find the
software at www.fftw.org, and detailed instructions at
www.gromacs.org.
Note that the default FFTW setup is double precision. Change the FFTW
configuration to single with --enable-float. If you want MPI
support,
use --enable-mpi. It is a good idea to install both single & double.
If your sysadm doesn't want to install it you can do it to a
location
in your home directory and provide the correct paths in ......
####################################################################
###############
With thanks !
B.Nataraj
--
David.
_____________________________________________________________________
___
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+++++
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
raja
raja_28 at fastmail.us
--
http://www.fastmail.fm - A fast, anti-spam email service.
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
raja
2006-04-03 08:28:29 UTC
Permalink
Dear Mr Erik,

No, I use fftw-3.0.1 and gromacs-3.0.1 and more I have not selected
FFTW-2 manually.

With thnaks
B.Nataraj

On Mon, 3 Apr 2006 10:05:53 +0200, "Erik Lindahl" <lindahl at sbc.su.se>
Post by Erik Lindahl
Hi,
Please read through and follow the detailed installation instructions at
http://www.gromacs.org/installation/index.php
Based in the limited output below it looks as if you are either
trying to install an earlier version of Gromacs without support for
FFTW-3, or you have manually selected FFTW-2.
Cheers,
Erik
Post by raja
Dear Mr.Spoel,
Thanks for your reply. Yea I checked , the corresponding files are
there is "/usr/local/lib". Totally 8 files and
1 folder called "pkgconfig". More I also tried to set envirnomental
variable to CPPFLAGS and LDFLAGS as command before configure but no
effect.
May I have to add these environmental variables in my .cshrc file ?.
Please suggest me any other flags to be enabled or disabled to make
configure to get path of fftw library files.
With thanks!
B.Nataraj
On Mon, 03 Apr 2006 09:06:22 +0200, "David van der Spoel"
Post by David van der Spoel
Post by raja
Dear gmxions,
I tried to compile gromacs in SGI IRIX6.5. I followed configuring and
installing of fftw, both single and double precision as per gromacs
website. When I tried to configure gromacs...it says.." Cannot find any
single precision fftw.h or sfftw.h". I also checked the
"/usr/local/include/". The folder contains 2 files "fftw3.f" and
"fftw3.h". More I had the experince of compiling under cygwin. So I did
crosscheck for files under folder in cygwin (/usr/local/include/ )
found exactly same files there too as "fftw3.f" and "fftw3.h". But the
configuration of gromacs worked in cygwin without any error, otherhand
why it fails in SGI ? Please help me out !
Maybe you explicitly have to add /usr/local/include to the CPPFLAGS
environment variable.
Do you have the corresponding libraries in /usr/local/lib?
Post by raja
I also pasted detailed error output while configuring gromacs in SGI.
####################################################################
###########
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... no
checking dynamic linker characteristics... irix6.5 ld.so
checking whether ln -s works... yes
checking for sqrt in -lm... yes
checking for fftw.h... no
checking for sfftw.h... no
configure: error: Cannot find any single precision fftw.h or sfftw.h
Do you have single precision FFTW installed? If you are using packages,
note that you also need fftw-devel to compile GROMACS. You can find the
software at www.fftw.org, and detailed instructions at
www.gromacs.org.
Note that the default FFTW setup is double precision. Change the FFTW
configuration to single with --enable-float. If you want MPI support,
use --enable-mpi. It is a good idea to install both single & double.
If your sysadm doesn't want to install it you can do it to a location
in your home directory and provide the correct paths in ......
####################################################################
###############
With thanks !
B.Nataraj
--
David.
_____________________________________________________________________
___
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+++++
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
raja
raja_28 at fastmail.us
--
http://www.fastmail.fm - A fast, anti-spam email service.
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
raja
raja_28 at fastmail.us
--
http://www.fastmail.fm - And now for something completely different
Erik Lindahl
2006-04-03 08:35:50 UTC
Permalink
Post by raja
Dear Mr Erik,
No, I use fftw-3.0.1 and gromacs-3.0.1 and more I have not selected
FFTW-2 manually.
Again, If you read the online installation instructions, it says
quite explicitly that Gromacs-3.3 and later supports FFTW3. You are
using an old Gromacs release with a new FFTW library.

Cheers,

Erik
raja
2006-04-03 09:06:32 UTC
Permalink
Dear Mr.Eriv and Mr.spoel ,
Thanks for your help. Sorry for unnessary confusion caused, I
just compared the version number as 3.0.1 , so I made mistake.
Now again I tried to configure groamcs3.3 , Now a new problem
has come up. The SGI which I am trying to install has its date
setback for some other reason. So when I try to configure
gromacs now, It shows following error.
###############################################################################################
checking build system type... mips-sgi-irix6.5
checking host system type... mips-sgi-irix6.5
checking for a BSD-compatible install... config/install-sh -c
checking whether build environment is sane... configure: error: newly
created file is older than distributed files!
Check your system clock
######################################################################################################

Please give me suggestion to configure without changing the current date
of the SGI.

With thanks!
B.Nataraj




On Mon, 3 Apr 2006 10:35:50 +0200, "Erik Lindahl" <lindahl at sbc.su.se>
Post by Erik Lindahl
Post by raja
Dear Mr Erik,
No, I use fftw-3.0.1 and gromacs-3.0.1 and more I have not selected
FFTW-2 manually.
Again, If you read the online installation instructions, it says
quite explicitly that Gromacs-3.3 and later supports FFTW3. You are
using an old Gromacs release with a new FFTW library.
Cheers,
Erik
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
raja
raja_28 at fastmail.us
--
http://www.fastmail.fm - I mean, what is it about a decent email service?
David van der Spoel
2006-04-03 09:09:55 UTC
Permalink
Post by raja
Dear Mr.Eriv and Mr.spoel ,
Thanks for your help. Sorry for unnessary confusion caused, I
just compared the version number as 3.0.1 , so I made mistake.
Now again I tried to configure groamcs3.3 , Now a new problem
has come up. The SGI which I am trying to install has its date
setback for some other reason. So when I try to configure
gromacs now, It shows following error.
###############################################################################################
checking build system type... mips-sgi-irix6.5
checking host system type... mips-sgi-irix6.5
checking for a BSD-compatible install... config/install-sh -c
checking whether build environment is sane... configure: error: newly
created file is older than distributed files!
Check your system clock
######################################################################################################
Please give me suggestion to configure without changing the current date
of the SGI.
restart from scratch
set the date on the distribution files after unpacking to the current
date on your machine using the "touch" command
Post by raja
With thanks!
B.Nataraj
On Mon, 3 Apr 2006 10:35:50 +0200, "Erik Lindahl" <lindahl at sbc.su.se>
Post by Erik Lindahl
Post by raja
Dear Mr Erik,
No, I use fftw-3.0.1 and gromacs-3.0.1 and more I have not selected
FFTW-2 manually.
Again, If you read the online installation instructions, it says
quite explicitly that Gromacs-3.3 and later supports FFTW3. You are
using an old Gromacs release with a new FFTW library.
Cheers,
Erik
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
raja
2006-04-03 09:49:09 UTC
Permalink
Dear Mr.Spoel,
Thanks for your help. It worked now but during compilation, the
following error occured .
##########################################################################################################
source='ghat.c' object='ghat.lo' libtool=yes \
DEPDIR=.deps depmode=sgi /bin/sh ../../config/depcomp \
/bin/sh ../../libtool --mode=compile --tag=CC cc -DHAVE_CONFIG_H
-I. -I. -I../../src -I../../include
-DGMXLIBDIR=\"/usr/local/gromacs/share/top\"
-I/usr/local/include -r12000 -mips4 -O3 -OPT:IEEE_arithmetic=3
-OPT:rsqrt=ON -SWP:loop_overhead -INLINE:=ON -LNO:opt=1
-LNO:ou_further=3 -OPT:Olimit=0:roundoff=3:alias=typed -woff
1174 -D__INLINE_INTRINSICS -c -o ghat.lo ghat.c
cc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include
-DGMXLIBDIR=\"/usr/local/gromacs/share/top\" -I/usr/local/include
-r12000 -mips4 -O3 -OPT:IEEE_arithmetic=3 -OPT:rsqrt=ON
-SWP:loop_overhead -INLINE:=ON -LNO:opt=1 -LNO:ou_further=3
-OPT:Olimit=0:roundoff=3:alias=typed -woff 1174 -D__INLINE_INTRINSICS
-c ghat.c -Wp,-MDupdate,.deps/ghat.TPlo -o ghat.o
cc-1515 cc: ERROR File = ghat.c, Line = 233
A value of type "int" cannot be assigned to an entity of type "real
***".

gh = mk_rgrid(ix,iy,iz);
^

1 error detected in the compilation of "ghat.c".
*** Error code 1 (bu21)
*** Error code 1 (bu21)
*** Error code 1 (bu21)
*** Error code 1 (bu21)
######################################################################################################################

With thanks !
B.Nataraj










On Mon, 03 Apr 2006 11:09:55 +0200, "David van der Spoel"
Post by David van der Spoel
Post by raja
Dear Mr.Eriv and Mr.spoel ,
Thanks for your help. Sorry for unnessary confusion caused, I
just compared the version number as 3.0.1 , so I made mistake.
Now again I tried to configure groamcs3.3 , Now a new problem
has come up. The SGI which I am trying to install has its date
setback for some other reason. So when I try to configure
gromacs now, It shows following error.
###############################################################################################
checking build system type... mips-sgi-irix6.5
checking host system type... mips-sgi-irix6.5
checking for a BSD-compatible install... config/install-sh -c
checking whether build environment is sane... configure: error: newly
created file is older than distributed files!
Check your system clock
######################################################################################################
Please give me suggestion to configure without changing the current date
of the SGI.
restart from scratch
set the date on the distribution files after unpacking to the current
date on your machine using the "touch" command
Post by raja
With thanks!
B.Nataraj
On Mon, 3 Apr 2006 10:35:50 +0200, "Erik Lindahl" <lindahl at sbc.su.se>
Post by Erik Lindahl
Post by raja
Dear Mr Erik,
No, I use fftw-3.0.1 and gromacs-3.0.1 and more I have not selected
FFTW-2 manually.
Again, If you read the online installation instructions, it says
quite explicitly that Gromacs-3.3 and later supports FFTW3. You are
using an old Gromacs release with a new FFTW library.
Cheers,
Erik
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________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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raja_28 at fastmail.us
--
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raja
2006-04-03 12:32:06 UTC
Permalink
Hi All,
I am reposting this eror again, as I could not find any proper solution
from the previous posting for the same error. I added #include
"fftgrid.h" in ghat.c as per
http://www.gromacs.org/pipermail/gmx-users/2006-February/019618.html but
ended up in different error of same kind as found in the posting
http://www.gromacs.org/pipermail/gmx-users/2006-February/019624.html.
And this topic is discontinued...No solution....So kindly let me know
the solution ?

With thanks !
B.Nataraj

##########################################################################################################

source='ghat.c' object='ghat.lo' libtool=yes \
DEPDIR=.deps depmode=sgi /bin/sh ../../config/depcomp \
/bin/sh ../../libtool --mode=compile --tag=CC cc -DHAVE_CONFIG_H
-I. -I. -I../../src -I../../include
-DGMXLIBDIR=\"/usr/local/gromacs/share/top\"
-I/usr/local/include -r12000 -mips4 -O3 -OPT:IEEE_arithmetic=3
-OPT:rsqrt=ON -SWP:loop_overhead -INLINE:=ON -LNO:opt=1
-LNO:ou_further=3 -OPT:Olimit=0:roundoff=3:alias=typed -woff
1174 -D__INLINE_INTRINSICS -c -o ghat.lo ghat.c
cc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include
-DGMXLIBDIR=\"/usr/local/gromacs/share/top\" -I/usr/local/include
-r12000 -mips4 -O3 -OPT:IEEE_arithmetic=3 -OPT:rsqrt=ON
-SWP:loop_overhead -INLINE:=ON -LNO:opt=1 -LNO:ou_further=3
-OPT:Olimit=0:roundoff=3:alias=typed -woff 1174 -D__INLINE_INTRINSICS
-c ghat.c -Wp,-MDupdate,.deps/ghat.TPlo -o ghat.o
cc-1515 cc: ERROR File = ghat.c, Line = 233
A value of type "int" cannot be assigned to an entity of type "real
***".

gh = mk_rgrid(ix,iy,iz);
^

1 error detected in the compilation of "ghat.c".
*** Error code 1 (bu21)
*** Error code 1 (bu21)
*** Error code 1 (bu21)
*** Error code 1 (bu21)
######################################################################################################################
--
raja
raja_28 at fastmail.us
--
http://www.fastmail.fm - Send your email first class
Tom Joseph
2006-04-03 17:50:24 UTC
Permalink
A wild guess: SGI's compiler doesn't support some language feature or
other in the same way as expected by the GROMACS source code. So, if
you have gcc installed, you might try compiling using that.

setenv CC `which gcc`
./configure --put-your-parameters-here

--Tom
Post by raja
Hi All,
I am reposting this eror again, as I could not find any proper
solution
from the previous posting for the same error. I added #include
"fftgrid.h" in ghat.c as per
http://www.gromacs.org/pipermail/gmx-users/2006-February/
019618.html but
ended up in different error of same kind as found in the posting
http://www.gromacs.org/pipermail/gmx-users/2006-February/019624.html.
And this topic is discontinued...No solution....So kindly let me know
the solution ?
With thanks !
B.Nataraj
######################################################################
####################################
source='ghat.c' object='ghat.lo' libtool=yes \
DEPDIR=.deps depmode=sgi /bin/sh ../../config/depcomp \
/bin/sh ../../libtool --mode=compile --tag=CC cc -
DHAVE_CONFIG_H
-I. -I. -I../../src -I../../include
-DGMXLIBDIR=\"/usr/local/gromacs/share/top\"
-I/usr/local/include -r12000 -mips4 -O3 -
OPT:IEEE_arithmetic=3
-OPT:rsqrt=ON -SWP:loop_overhead -INLINE:=ON -LNO:opt=1
-LNO:ou_further=3 -OPT:Olimit=0:roundoff=3:alias=typed -woff
1174 -D__INLINE_INTRINSICS -c -o ghat.lo ghat.c
cc -DHAVE_CONFIG_H -I. -I. -I../../src -I../../include
-DGMXLIBDIR=\"/usr/local/gromacs/share/top\" -I/usr/local/include
-r12000 -mips4 -O3 -OPT:IEEE_arithmetic=3 -OPT:rsqrt=ON
-SWP:loop_overhead -INLINE:=ON -LNO:opt=1 -LNO:ou_further=3
-OPT:Olimit=0:roundoff=3:alias=typed -woff 1174 -D__INLINE_INTRINSICS
-c ghat.c -Wp,-MDupdate,.deps/ghat.TPlo -o ghat.o
cc-1515 cc: ERROR File = ghat.c, Line = 233
A value of type "int" cannot be assigned to an entity of type "real
***".
gh = mk_rgrid(ix,iy,iz);
^
1 error detected in the compilation of "ghat.c".
*** Error code 1 (bu21)
*** Error code 1 (bu21)
*** Error code 1 (bu21)
*** Error code 1 (bu21)
######################################################################
################################################
--
raja
raja_28 at fastmail.us
--
http://www.fastmail.fm - Send your email first class
_______________________________________________
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David van der Spoel
2006-04-03 08:06:12 UTC
Permalink
Post by raja
Dear Mr.Spoel,
Thanks for your reply. Yea I checked , the corresponding files are
there is "/usr/local/lib". Totally 8 files and
including the libfftw3.a and libfftw3f.a ?
Post by raja
1 folder called "pkgconfig". More I also tried to set envirnomental
variable to CPPFLAGS and LDFLAGS as command before configure but no
effect.
May I have to add these environmental variables in my .cshrc file ?.
Do you use the csh or sh?
Post by raja
Please suggest me any other flags to be enabled or disabled to make
configure to get path of fftw library files.
Do also check the archives, SGI are problematic...
--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
raja
2006-04-03 08:38:04 UTC
Permalink
Post by David van der Spoel
including the libfftw3.a and libfftw3f.a ?
yea the above said both files, libfftw3.a and libfftw3f.a are there in
/usr/local/lib.
Post by David van der Spoel
Do you use the csh or sh?
I am using csh shell.

With thanks !
B.Nataraj
___________________________________________
--
raja
raja_28 at fastmail.us
--
http://www.fastmail.fm - mmm... Fastmail...
David van der Spoel
2006-04-03 07:07:44 UTC
Permalink
Post by yoshizawa006
Dear David,
thank you very much for your reply!
Indeed I have used -type dihedral.
Could it be, the problem lies in the [].tpr and [].xtc files? I mean,
which subset of atoms must I choose in those files? (This very part of
the previous discussion was obscure to me!)
for the g_angle analysis you need the normal tpr file.
for the g_covar you need a dummy tpr file with 2n/3 atoms where n is the
number of dihedrals you want to analyze.
Post by yoshizawa006
Best wishes!
Maki Yoshizawa
Post by yoshizawa006
Hello,
I would like to use PCA analysis in the dihedral space.
Despite having read the topics related to this issue in the
GROMACS page
Post by yoshizawa006
I am not quite sure how to accomplish this :-)
The -or option in the g_angle (version 3.3) seems not to be
working. I
Post by yoshizawa006
am already using an index file as sugested in the archives.
more info please.
did you use -type dihedral ?
Post by yoshizawa006
Best wishes
Maki Yoshizawa
------------------------------------------------------------------------
Post by yoshizawa006
Celebrate Yahoo! JAPAN 10th Anniversary
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Post by yoshizawa006
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David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
_______________________________________________
gmx-users mailing list gmx-users at gromacs.org
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Celebrate Yahoo! JAPAN 10th Anniversary
<http://pr.mail.yahoo.co.jp/10thann/>
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
yoshizawa006
2006-04-03 12:18:03 UTC
Permalink
Dear David,

thank you ver much!

As a matter of fact, g_angle (3.3) is working perfectly well! It was a stupid error of mine!!

Sorry for the inconvenience...

Best wishes!

Maki Yoshizawa









---------------------------------
Celebrate Yahoo! JAPAN 10th Anniversary
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