[gmx-users] Unexpected behavior of g_msd

[Berk Hess]

Hi,

You don't need trjconv, g_msd has options -b and -e.
But the regression is obviously done on the time differences and not on
the frame times. MSD is a function of a time difference, not of simulation time.

Berk


> Date: Thu, 26 Nov 2009 13:24:12 +1100
> From: Dallas.Warren at pharm.monash.edu.au
> Subject: RE: [gmx-users] Unexpected behavior of g_msd
> To: gmx-users at gromacs.org
> 
> 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
> > 
> > --
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before
> > posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> -- 
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
 		 	   		  
_________________________________________________________________
New Windows 7: Simplify what you do everyday. Find the right PC for you.
http://windows.microsoft.com/shop
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20091126/886ea377/attachment.html>