[gmx-users] Unexpected behavior of g_msd

[Darrell Koskinen]

Hi Tsjerk,
I looked at the .trr file and cannot read this file and simply delete 
lines to create a sub-trajectory. So, how do I create a sub-trajectory 
to analyze?

Thanks.

Darrell

Date: Wed, 25 Nov 2009 09:04:01 +0100 From: Tsjerk Wassenaar 
<tsjerkw at gmail.com> Subject: Re: [gmx-users] Unexpected behavior of 
g_msd To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Message-ID: 
<8ff898150911250004l42fee014qf3298816c9ef3db3 at mail.gmail.com> 
Content-Type: text/plain; charset=ISO-8859-1 Hi Darrell, You can check 
whether the output is identical to a trajectory of the specified 
frames... It may well be that the counting for the regression is done on 
the frames read: 100 - 60 = 40 ps Then 4 and 35.9 would correspond to 64 
and 95.9. The answer is in the code... But using a subtrajectory may 
give you good hint. Hope it helps, Tsjerk On Wed, Nov 25, 2009 at 7:42 
AM, Darrell Koskinen <darrellk at ece.ubc.ca> wrote:

> > Dear GROMACS-ites,
> > I am a little confused by the behavior of g_msd. I have a trr file with data
> > points from t=0 to t=100 ps and thought that the following command would
> > perform a regression for the data points between t=60 ps and t=100 ps to
> > determine the diffision constant of the ammonia gas in the simualtion:
> >
> > *g_msd -f mdtraj.trr -s mdtopol.tpr -type x -b 60 -e 100*
> >
> > However, the output:
> > *
> > /trn version: GMX_trn_file (single precision)
> > Reading frame     900 time   90.000
> >
> > Used 4 restart points spaced 10 ps over 39.9 ps
> >
> > Fitting from 4 to 35.9 ps
> >
> > D[       NH3] 3625.5647 (+/- 2802.0500) 1e-5 cm2/s
> > /*
> > seems to indicate that the regression was performed between t=4 ps and
> > t=35.9 ps.
> >
> > Could you please explain to me what is happening?
> >
> > Thanks.
> >
> > Darrell