Re: [gmx-users] gmxcheck

Thanks Justin very much for your help. (Extremely silly and unthoughtful of me to forget this) Kind regards, Ankita On Mon, Nov 4, 2013 at 12:40 PM, Justin Lemkul wrote: > > > On 11/4/13 7:37 AM, Ankita Naithani wrote: > >> I do have the .mdp file. Main thing I was concerned about were detai

Re: [gmx-users] gmxcheck

On 11/4/13 7:37 AM, Ankita Naithani wrote: I do have the .mdp file. Main thing I was concerned about were details like number of water molecules added and number of counter ions added. Does gmxdump output that information? Yes, buried in a long list of other things. Trivial details like tha

Re: [gmx-users] gmxcheck

I do have the .mdp file. Main thing I was concerned about were details like number of water molecules added and number of counter ions added. Does gmxdump output that information? On Mon, Nov 4, 2013 at 12:19 PM, Justin Lemkul wrote: > > > On 11/4/13 7:14 AM, Ankita Naithani wrote: > >> Hi Ju

Re: [gmx-users] gmxcheck

On 11/4/13 7:14 AM, Ankita Naithani wrote: Hi Justin, Thank you for your reply. I did give the .tpr file but the job terminated after few frames only. Also, if that is not helpful, do you have any There are no frames in a .tpr file. I suspect you're simply issuing the command incorrectly,

Re: [gmx-users] gmxcheck

Hi Justin, Thank you for your reply. I did give the .tpr file but the job terminated after few frames only. Also, if that is not helpful, do you have any suggestions to recover the essential information which you would include as part of methods? Kind regards, Ankita On Mon, Nov 4, 2013 at 12:

Re: [gmx-users] gmxcheck

On 11/4/13 5:06 AM, Ankita Naithani wrote: Hi, I was wondering if anyone could help me with the gmxcheck function? In the manual it is written, -m flag is given a LaTeX file will be written consisting of a rough outline for a methods section for a paper. I tried it several times but there isn'

[gmx-users] gmxcheck

Hi, I was wondering if anyone could help me with the gmxcheck function? In the manual it is written, -m flag is given a LaTeX file will be written consisting of a rough outline for a methods section for a paper. I tried it several times but there isn't any file that I can see. I had run some simu

Re: [gmx-users] gmxcheck and GROMOS96 bonds

Will do, thank you for fast response! Reid On Tue, Jan 8, 2013 at 11:11 AM, Justin Lemkul wrote: > > > On 1/8/13 10:56 AM, Reid Van Lehn wrote: > >> Hi Gromacs users, >> >> I was using gmxcheck to check a simple trajectory of surfactants, and get >> many errors of the type "Distance between ato

Re: [gmx-users] gmxcheck and GROMOS96 bonds

On 1/8/13 10:56 AM, Reid Van Lehn wrote: Hi Gromacs users, I was using gmxcheck to check a simple trajectory of surfactants, and get many errors of the type "Distance between atoms X and Y is 0.153, should be 0.023" where the actual distance is always approximately correct and the "correct" va

Re: [gmx-users] gmxcheck and trjconv

enaar" <[EMAIL PROTECTED]> Date: Wednesday, March 7, 2007 5:56 pm Subject: Re: [gmx-users] gmxcheck and trjconv > Hey Andrea, > > Also note that you have 70 FRAMES with 1 ps time step. That means, > with the first frame at t=0, that you have a maximum time of (70-1)*1 > ps =

Re: [gmx-users] gmxcheck and trjconv

Hey Andrea, Also note that you have 70 FRAMES with 1 ps time step. That means, with the first frame at t=0, that you have a maximum time of (70-1)*1 ps = 69 ps in the output. Ciao! Tsjerk On 3/7/07, David van der Spoel <[EMAIL PROTECTED]> wrote: andrea spitaleri wrote: > Hi, > however in md0.

Re: [gmx-users] gmxcheck and trjconv

andrea spitaleri wrote: Hi, however in md0.log the right time is reported (69 and not 70) and David van der Spoel wrote: andrea spitaleri wrote: Hi all, silly question. I have checked a trr with gmxcheck and I get this output below: Item#frames Timestep (ps) Step701 Ti

Re: [gmx-users] gmxcheck and trjconv

Hi, however in md0.log the right time is reported (69 and not 70) and David van der Spoel wrote: > andrea spitaleri wrote: >> Hi all, >> silly question. I have checked a trr with gmxcheck and I get this >> output below: >> Item#frames Timestep (ps) >> Step701 >> Time

Re: [gmx-users] gmxcheck and trjconv

Hi nope they are both finished. I have also checked the edr files and the time does not correspond to the time found in the respectively trr files. Those MD are carried out in a supercomputer (SARA in Amsterdam) and they were killed by the queue system. Probably as you said a buffer problem ...

Re: [gmx-users] gmxcheck and trjconv

andrea spitaleri wrote: Hi all, silly question. I have checked a trr with gmxcheck and I get this output below: Item#frames Timestep (ps) Step701 Time701 Lambda 701 Coords 701 Velocities 243 Forces 0 Box

[gmx-users] gmxcheck and trjconv

Hi all, silly question. I have checked a trr with gmxcheck and I get this output below: Item#frames Timestep (ps) Step701 Time701 Lambda 701 Coords 701 Velocities 243 Forces 0 Box 701 however if th