[gmx-users] Unexpected behavior of g_msd

Berk Hess gmx3 at hotmail.com
Thu Nov 26 11:34:02 CET 2009 

NO!
The MSD is NOT a function of the trajectory time!
The MSD is a function of time differences.
For example:
if trestart=10 and -b=60 then MSD(4) in the output is the average of the the MSD
between 64 and 68, 74 and 78, 84 and 88, etc.

Berk

> Date: Thu, 26 Nov 2009 01:52:17 -0800
> From: darrellk at ece.ubc.ca
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Unexpected behavior of g_msd
> 
> Hi Berk, Yes, I am aware of the -b and -e options in g_msd but was 
> wondering why the output said "Fitting from 4 to 35.9 ps" when I 
> selected the time period from 60 to 100 ps. It appears that the output 
> comment actually meant that it was fitting from 60+4 to 60+35.9 ps, but 
> this is not clear to the user. At least, it was not obvious to me. When 
> you say "MSD is a function of a time difference, not of simulation 
> time", so you mean that I do not need to simulate for a longer period of 
> time to get accurate results? Do I simply need to change trestart to a 
> smaller value? Or is there something else I must do? Thanks. Darrell 
> Date: Thu, 26 Nov 2009 10:27:27 +0100 From: Berk Hess <gmx3 at hotmail.com> 
> Subject: RE: [gmx-users] Unexpected behavior of g_msd To: Discussion 
> list for GROMACS users <gmx-users at gromacs.org> Message-ID: 
> <COL113-W13EFECFADFB96DB6D2356B8E9B0 at phx.gbl> Content-Type: text/plain; 
> charset="iso-8859-1" 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
> >>>>         
> -- 
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