[gmx-users] Unexpected behavior of g_msd

[Dallas B. Warren]

trjconv

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at pharm.monash.edu.au
+61 3 9903 9167
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble
a nail. 


> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-
> bounces at gromacs.org] On Behalf Of Darrell Koskinen
> Sent: Thursday, 26 November 2009 12:48 PM
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Unexpected behavior of g_msd
> 
> 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
> 
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