Discussion:
Problem with PME
(too old to reply)
Srikrishna Sureshkumar
2006-02-22 07:10:47 UTC
Permalink
Dear All

I am new user to gromacs and i was trying to use the coloumbtype PME.
When ever I use this type with the integrator Steep the simulation runs for
ever. No output is generated it appears like the system is being put in the
leep mode.

I am ataching my MDP file. I would like to know if there is any correction I
could do so that i can do my simulation properly. At the same time if I use
coloubtype cut-off instaed of PME the simulation goes on properly and the
only problem is that it does not converge in a single run.

Thanks and Regards

S. Srikrishna
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David van der Spoel
2006-02-22 07:43:20 UTC
Permalink
Post by Srikrishna Sureshkumar
Dear All
I am new user to gromacs and i was trying to use the coloumbtype PME.
When ever I use this type with the integrator Steep the simulation runs
for ever. No output is generated it appears like the system is being put
in the leep mode.
Are you running this on SGI?

I'm not sure what it could be, the mdp file is fine.
Post by Srikrishna Sureshkumar
I am ataching my MDP file. I would like to know if there is any
correction I could do so that i can do my simulation properly. At the
same time if I use coloubtype cut-off instaed of PME the simulation goes
on properly and the only problem is that it does not converge in a
single run.
Thanks and Regards
S. Srikrishna
------------------------------------------------------------------------
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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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Srikrishna Sureshkumar
2006-02-22 10:07:45 UTC
Permalink
Dear David,

No, I am runing this on a Intel P3 System with redhat 7.2.

Regards
Srikrishna
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David van der Spoel
2006-02-22 11:00:51 UTC
Permalink
Post by Srikrishna Sureshkumar
Dear David,
No, I am runing this on a Intel P3 System with redhat 7.2.
And did you compile gromacs and fftw yourself?
Post by Srikrishna Sureshkumar
Regards
Srikrishna
------------------------------------------------------------------------
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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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
S. Srikrishna
2006-02-23 02:23:14 UTC
Permalink
Dear David
Post by David van der Spoel
And did you compile gromacs and fftw yourself?
No. System admisitrator did that. If it is a installation problem even with
coloumbtype "cut-off" it shouldnt work.
And PME works some times with integrator "md".

Regards
Srikrishna
David van der Spoel
2006-02-22 13:13:34 UTC
Permalink
Post by Srikrishna Sureshkumar
Dear David
Post by David van der Spoel
And did you compile gromacs and fftw yourself?
No. System admisitrator did that. If it is a installation problem even
with coloumbtype "cut-off" it shouldnt work.
And PME works some times with integrator "md".
Sometimes there can be problems with multiple installed FFTW libraries,
i.e. you link against one library and use another.

It is difficult to debug, but the installation is the first suspect. If
you say it sometimes works, does it work reproducibly? If not you might
have a hardware problem.
Post by Srikrishna Sureshkumar
Regards
Srikrishna
_______________________________________________
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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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Daniela S. Mueller
2006-02-23 03:10:35 UTC
Permalink
hi s.,

as you are using the integrator steep, i assume you are running energy
minimisations?
in that case i suspect that the type of coulomb-interaction model is not
critical, so you can set it to cut-off.
what i have found is that energy minimisation doesn't work with
coulomb-type = (generalised) reaction-field, so it might be the same
case with pme.

@david van der spoel: is this a bug?

best regards and good luck,
daniela
Post by Srikrishna Sureshkumar
Dear All
I am new user to gromacs and i was trying to use the coloumbtype PME.
When ever I use this type with the integrator Steep the simulation
runs for ever. No output is generated it appears like the system is
being put in the leep mode.
I am ataching my MDP file. I would like to know if there is any
correction I could do so that i can do my simulation properly. At the
same time if I use coloubtype cut-off instaed of PME the simulation
goes on properly and the only problem is that it does not converge in
a single run.
Thanks and Regards
S. Srikrishna
--
Daniela S. Mueller

biologist (Diplom, German degree)
______________________________________________________________________

- Molecular Dynamics Group, UQ -

Address:
School of Molecular and Microbial Sciences (SMMS)
Chemistry Building (#68)
University of Queensland
Qld 4072, Brisbane
Australia

Phone: +61-7-33653732

Website: http://ilc00f.facbacs.uq.edu.au/SMMS/a_mark/Front.htm

**********************************************************************

- MD group, RuG -

Address:
Molecular Dynamics
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747 AG Groningen
The Netherlands

Website: http://www.rug.nl/gbb/md
______________________________________________________________________
David Mobley
2006-02-25 15:29:25 UTC
Permalink
Minimization generally works fine for me with PME, so I would suspect
either the system topology/coordinates or the GROMACS installation,
rather than a bug. I do steepest descents minimization with PME all
the time.

David
Post by Daniela S. Mueller
hi s.,
as you are using the integrator steep, i assume you are running energy
minimisations?
in that case i suspect that the type of coulomb-interaction model is not
critical, so you can set it to cut-off.
what i have found is that energy minimisation doesn't work with
coulomb-type = (generalised) reaction-field, so it might be the same
case with pme.
@david van der spoel: is this a bug?
best regards and good luck,
daniela
Post by Srikrishna Sureshkumar
Dear All
I am new user to gromacs and i was trying to use the coloumbtype PME.
When ever I use this type with the integrator Steep the simulation
runs for ever. No output is generated it appears like the system is
being put in the leep mode.
I am ataching my MDP file. I would like to know if there is any
correction I could do so that i can do my simulation properly. At the
same time if I use coloubtype cut-off instaed of PME the simulation
goes on properly and the only problem is that it does not converge in
a single run.
Thanks and Regards
S. Srikrishna
--
Daniela S. Mueller
biologist (Diplom, German degree)
______________________________________________________________________
- Molecular Dynamics Group, UQ -
School of Molecular and Microbial Sciences (SMMS)
Chemistry Building (#68)
University of Queensland
Qld 4072, Brisbane
Australia
Phone: +61-7-33653732
Website: http://ilc00f.facbacs.uq.edu.au/SMMS/a_mark/Front.htm
**********************************************************************
- MD group, RuG -
Molecular Dynamics
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747 AG Groningen
The Netherlands
Website: http://www.rug.nl/gbb/md
______________________________________________________________________
_______________________________________________
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.
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