Re: [gmx-users] snapshot

2013-07-15 Thread Rama Krishna Koppisetti
Thank you very much *Justin*. -- Rama On Mon, Jul 15, 2013 at 8:06 AM, Justin Lemkul 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 do in

Re: [gmx-users] snapshot

2013-07-15 Thread Justin Lemkul
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. g_t

Re: [gmx-users] snapshot

2013-07-15 Thread Rama Krishna Koppisetti
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 -d

Re: [gmx-users] snapshot

2013-07-15 Thread Dr. Vitaly Chaban
look for either "-dt" or "-skip". Dr. Vitaly V. Chaban On Mon, Jul 15, 2013 at 2:03 AM, 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. > > > > -- > View

Re: [gmx-users] snapshot

2013-07-14 Thread Justin Lemkul
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 w

Re: [gmx-users] Snapshot and co-ordinate query

2013-06-06 Thread Ankita naithani
Hi Justin, Thank you so much for the clarification. Kind regards, Ankita On Wed, Jun 5, 2013 at 11:28 PM, Justin Lemkul 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 >> si

Re: [gmx-users] Snapshot and co-ordinate query

2013-06-05 Thread Justin Lemkul
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 T

Re: [gmx-users] Snapshot taken under certain condition

2009-10-06 Thread Arik Cohen
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 you'l

Re: [gmx-users] Snapshot taken under certain condition

2009-10-06 Thread Mark Abraham
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 (dangerous

Re: [gmx-users] Snapshot taken under certain condition

2009-10-06 Thread Arik Cohen
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, bu

Re: [gmx-users] Snapshot taken under certain condition

2009-10-06 Thread Justin A. Lemkul
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 a