look for either -dt or -skip.
Dr. Vitaly V. Chaban
On Mon, Jul 15, 2013 at 2:03 AM, Rama ramkishn...@gmail.com wrote:
Hi,
How to get a snapshots in equal intervals of time (250ps) from production
MD
trajectory. I'm using -sep , -t0, -timestep but output came only one .gro
file.
--
Hi,
The following command I used for the snapshots but I'm getting one frame
time 0 time 500. what are the changes I need to do in the command to get
snapshots in equal intervals of time for ex: 250ps. My production MD
trajectory was 15ns.
g_trjconv -s md.tpr -f md.trr -o beta.gro -skip 1 -dt 0
On 7/15/13 9:02 AM, Rama Krishna Koppisetti wrote:
Hi,
The following command I used for the snapshots but I'm getting one frame
time 0 time 500. what are the changes I need to do in the command to get
snapshots in equal intervals of time for ex: 250ps. My production MD
trajectory was 15ns.
Thank you very much *Justin*.
--
Rama
On Mon, Jul 15, 2013 at 8:06 AM, Justin Lemkul jalem...@vt.edu wrote:
On 7/15/13 9:02 AM, Rama Krishna Koppisetti wrote:
Hi,
The following command I used for the snapshots but I'm getting one frame
time 0 time 500. what are the changes I need to
Hi,
How to get a snapshots in equal intervals of time (250ps) from production MD
trajectory. I'm using -sep , -t0, -timestep but output came only one .gro
file.
--
View this message in context:
http://gromacs.5086.x6.nabble.com/snapshot-tp5009837.html
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On 7/14/13 9:03 PM, Rama wrote:
Hi,
How to get a snapshots in equal intervals of time (250ps) from production MD
trajectory. I'm using -sep , -t0, -timestep but output came only one .gro
file.
trjconv -skip -sep should work, but without exact command lines and the output
you received (as
Hi Justin,
Thank you so much for the clarification.
Kind regards,
Ankita
On Wed, Jun 5, 2013 at 11:28 PM, Justin Lemkul jalem...@vt.edu wrote:
On 6/5/13 3:03 PM, Ankita naithani wrote:
Hi,
I have two questions.
I have performed a simulation on my protein structure and after the
Hi,
I have two questions.
I have performed a simulation on my protein structure and after the
simulation, I used trjconv to obtain snapshots after every 10 ns with the
following command:
trjconv -f md.xtc -s md.tpr -b 1 -e 10001 -o md_10.pdb
and chose 0 (system) for the group.
However,
On 6/5/13 3:03 PM, Ankita naithani wrote:
Hi,
I have two questions.
I have performed a simulation on my protein structure and after the
simulation, I used trjconv to obtain snapshots after every 10 ns with the
following command:
trjconv -f md.xtc -s md.tpr -b 1 -e 10001 -o md_10.pdb
Dear users,
Is there a way(in the mdp file) to take a snapshot of only the C-alpha
atoms along a trajectory if certain condition are met(tested every time
a snapshot needs to be taken) ?
Thanks
Arik
___
gmx-users mailing list
Arik Cohen wrote:
Dear users,
Is there a way(in the mdp file) to take a snapshot of only the C-alpha
atoms along a trajectory if certain condition are met(tested every time
a snapshot needs to be taken) ?
No, but you could probably script it after the trajectory is run, using whatever
Thanks for all your help and rapid response.
Arik
Justin A. Lemkul wrote:
Arik Cohen wrote:
Dear users,
Is there a way(in the mdp file) to take a snapshot of only the
C-alpha atoms along a trajectory if certain condition are met(tested
every time a snapshot needs to be taken) ?
No,
Arik Cohen wrote:
Dear users,
Is there a way(in the mdp file) to take a snapshot of only the C-alpha
atoms along a trajectory if certain condition are met(tested every time
a snapshot needs to be taken) ?
If you know in advance you'll only ever want the C-alpha atoms for
analysis
Thanks allot for all your help
Arik
Mark Abraham wrote:
Arik Cohen wrote:
Dear users,
Is there a way(in the mdp file) to take a snapshot of only the
C-alpha atoms along a trajectory if certain condition are met(tested
every time a snapshot needs to be taken) ?
If you know in advance
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