[gmx-users] Regarding trajectory file

[Ravi Kumar Venkatraman]

Dear All,
I have ran a 10 ns production run for chloranil in 500
methanol solvent box. I want to get the coordinates of solvent and solute
at different time steps from the trajectory file (*.xtc). Can anybody tell
me how to extract the details using VMD or any other viewer.

Thank you in advance

*With Regards,
Ravi Kumar Venkatraman,
IPC Dept., IISc,
Bangalore, INDIA.

[phone].*
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[Mark Abraham]

Post by Ravi Kumar Venkatraman
Dear All,
I have ran a 10 ns production run for chloranil in 500
methanol solvent box. I want to get the coordinates of solvent and
solute at different time steps from the trajectory file (*.xtc). Can
anybody tell me how to extract the details using VMD or any other viewer.

You're unlikely to get help for non-GROMACS software on this mailing
list. Check out manual section 7.4 for clues on what GROMACS tools might
help, and then section 8 and appendix D for more details.

Mark

[aiswarya pawar]

You can write this on VMD forum. Anyways you can try by doing this in the
Tcl console-

set sel [atomselect top "solvent"]
$sel get {x y z}

This would give you the coordinates of the solvent, for your purpose you
got to iterate so as to get for each time step.


Aiswarya
SERC Dept, IISc
Bangalore

Post by Ravi Kumar Venkatraman
Dear All,
I have ran a 10 ns production run for chloranil in 500
methanol solvent box. I want to get the coordinates of solvent and solute
at different time steps from the trajectory file (*.xtc). Can anybody tell
me how to extract the details using VMD or any other viewer.

You're unlikely to get help for non-GROMACS software on this mailing list.
Check out manual section 7.4 for clues on what GROMACS tools might help,
and then section 8 and appendix D for more details.
Mark
--
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[Rausch, Felix]

Or you could use trjconv in a little script to convert the snapshots you
like to .pbd. Use the -b and -e flags to choose the respective time
points.

Also see
http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts
for the use trjconv non-interactively.



Good luck.



Von: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] Im Auftrag von aiswarya pawar
Gesendet: Mittwoch, 18. Januar 2012 07:53
An: Discussion list for GROMACS users
Betreff: Re: [gmx-users] Regarding trajectory file



You can write this on VMD forum. Anyways you can try by doing this in
the Tcl console-

set sel [atomselect top "solvent"]
$sel get {x y z}

This would give you the coordinates of the solvent, for your purpose you
got to iterate so as to get for each time step.


Aiswarya
SERC Dept, IISc
Bangalore




On Wed, Jan 18, 2012 at 12:06 PM, Mark Abraham <Mark.Abraham at anu.edu.au>
wrote:

On 18/01/2012 5:31 PM, Ravi Kumar Venkatraman wrote:


Dear All,
I have ran a 10 ns production run for chloranil in 500
methanol solvent box. I want to get the coordinates of solvent and
solute at different time steps from the trajectory file (*.xtc). Can
anybody tell me how to extract the details using VMD or any other
viewer.



You're unlikely to get help for non-GROMACS software on this mailing
list. Check out manual section 7.4 for clues on what GROMACS tools might
help, and then section 8 and appendix D for more details.

Mark
--
gmx-users mailing list gmx-users at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
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[Justin A. Lemkul]

Post by Rausch, Felix
Or you could use trjconv in a little script to convert the snapshots you
like to .pbd. Use the ?b and ?e flags to choose the respective time points.
Also see
http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts
for the use trjconv non-interactively.

Or, more directly, just trjconv -dump.

-Justin
--
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | [phone]
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================

[Mirco Wahab]

Post by Ravi Kumar Venkatraman
Dear All,
I have ran a 10 ns production run for chloranil in 500 methanol solvent box. I want to get the coordinates of solvent and solute at different time steps from the trajectory file (*.xtc). Can anybody tell me how to extract the details using

In the directory of the xtc file, the (2'nd) command

$> mkdir GRO
$> trjconv -noh -novel -skip 1 -sep -nzero 4 -o GRO/out.gro

will save every single frame of your simulation in
a .gro file into a subdirectory GRO/

If you don't wan't every single frame, use
"-skip 2" in the above option to get every
second frame.

mwa