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NO!<br>The MSD is NOT a function of the trajectory time!<br>The MSD is a function of time differences.<br>For example:<br>if trestart=10 and -b=60 then MSD(4) in the output is the average of the the MSD<br>between 64 and 68, 74 and 78, 84 and 88, etc.<br><br>Berk<br><br>> Date: Thu, 26 Nov 2009 01:52:17 -0800<br>> From: darrellk@ece.ubc.ca<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] Unexpected behavior of g_msd<br>> <br>> Hi Berk, Yes, I am aware of the -b and -e options in g_msd but was <br>> wondering why the output said "Fitting from 4 to 35.9 ps" when I <br>> selected the time period from 60 to 100 ps. It appears that the output <br>> comment actually meant that it was fitting from 60+4 to 60+35.9 ps, but <br>> this is not clear to the user. At least, it was not obvious to me. When <br>> you say "MSD is a function of a time difference, not of simulation <br>> time", so you mean that I do not need to simulate for a longer period of <br>> time to get accurate results? Do I simply need to change trestart to a <br>> smaller value? Or is there something else I must do? Thanks. Darrell <br>> Date: Thu, 26 Nov 2009 10:27:27 +0100 From: Berk Hess <gmx3@hotmail.com> <br>> Subject: RE: [gmx-users] Unexpected behavior of g_msd To: Discussion <br>> list for GROMACS users <gmx-users@gromacs.org> Message-ID: <br>> <COL113-W13EFECFADFB96DB6D2356B8E9B0@phx.gbl> Content-Type: text/plain; <br>> charset="iso-8859-1" Hi, You don't need trjconv, g_msd has options -b <br>> and -e. But the regression is obviously done on the time differences and <br>> not on the frame times. MSD is a function of a time difference, not of <br>> simulation time. Berk<br>> <br>> > > Date: Thu, 26 Nov 2009 13:24:12 +1100<br>> > > From: Dallas.Warren@pharm.monash.edu.au<br>> > > Subject: RE: [gmx-users] Unexpected behavior of g_msd<br>> > > To: gmx-users@gromacs.org<br>> > > <br>> > > trjconv<br>> > > <br>> > > Catch ya,<br>> > > <br>> > > Dr. Dallas Warren<br>> > > Drug Delivery, Disposition and Dynamics<br>> > > Monash Institute of Pharmaceutical Sciences, Monash University<br>> > > 381 Royal Parade, Parkville VIC 3010<br>> > > dallas.warren@pharm.monash.edu.au<br>> > > +61 3 9903 9167<br>> > > ---------------------------------<br>> > > When the only tool you own is a hammer, every problem begins to resemble<br>> > > a nail. <br>> > > <br>> > > <br>> > <br>> >> > > -----Original Message-----<br>> >> > > From: gmx-users-bounces@gromacs.org [mailto:gmx-users-<br>> >> > > bounces@gromacs.org] On Behalf Of Darrell Koskinen<br>> >> > > Sent: Thursday, 26 November 2009 12:48 PM<br>> >> > > To: gmx-users@gromacs.org<br>> >> > > Subject: [gmx-users] Unexpected behavior of g_msd<br>> >> > > <br>> >> > > Hi Tsjerk,<br>> >> > > I looked at the .trr file and cannot read this file and simply delete<br>> >> > > lines to create a sub-trajectory. So, how do I create a sub-trajectory<br>> >> > > to analyze?<br>> >> > > <br>> >> > > Thanks.<br>> >> > > <br>> >> > > Darrell<br>> >> > > <br>> >> > > Date: Wed, 25 Nov 2009 09:04:01 +0100 From: Tsjerk Wassenaar<br>> >> > > <tsjerkw@gmail.com> Subject: Re: [gmx-users] Unexpected behavior of<br>> >> > > g_msd To: Discussion list for GROMACS users <gmx-users@gromacs.org><br>> >> > > Message-ID:<br>> >> > > <8ff898150911250004l42fee014qf3298816c9ef3db3@mail.gmail.com><br>> >> > > Content-Type: text/plain; charset=ISO-8859-1 Hi Darrell, You can check<br>> >> > > whether the output is identical to a trajectory of the specified<br>> >> > > frames... It may well be that the counting for the regression is done<br>> >> > > on<br>> >> > > the frames read: 100 - 60 = 40 ps Then 4 and 35.9 would correspond to<br>> >> > > 64<br>> >> > > and 95.9. The answer is in the code... But using a subtrajectory may<br>> >> > > give you good hint. Hope it helps, Tsjerk On Wed, Nov 25, 2009 at 7:42<br>> >> > > AM, Darrell Koskinen <darrellk@ece.ubc.ca> wrote:<br>> >> > > <br>> >> <br>> >>>> > > > > Dear GROMACS-ites,<br>> >>>> > > > > I am a little confused by the behavior of g_msd. I have a trr file<br>> >>>> <br>> >> > > with data<br>> >> <br>> >>>> > > > > points from t=0 to t=100 ps and thought that the following command<br>> >>>> <br>> >> > > would<br>> >> <br>> >>>> > > > > perform a regression for the data points between t=60 ps and t=100<br>> >>>> <br>> >> > > ps to<br>> >> <br>> >>>> > > > > determine the diffision constant of the ammonia gas in the<br>> >>>> <br>> >> > > simualtion:<br>> >> <br>> >>>> > > > ><br>> >>>> > > > > *g_msd -f mdtraj.trr -s mdtopol.tpr -type x -b 60 -e 100*<br>> >>>> > > > ><br>> >>>> > > > > However, the output:<br>> >>>> > > > > *<br>> >>>> > > > > /trn version: GMX_trn_file (single precision)<br>> >>>> > > > > Reading frame 900 time 90.000<br>> >>>> > > > ><br>> >>>> > > > > Used 4 restart points spaced 10 ps over 39.9 ps<br>> >>>> > > > ><br>> >>>> > > > > Fitting from 4 to 35.9 ps<br>> >>>> > > > ><br>> >>>> > > > > D[ NH3] 3625.5647 (+/- 2802.0500) 1e-5 cm2/s<br>> >>>> > > > > /*<br>> >>>> > > > > seems to indicate that the regression was performed between t=4 ps<br>> >>>> <br>> >> > > and<br>> >> <br>> >>>> > > > > t=35.9 ps.<br>> >>>> > > > ><br>> >>>> > > > > Could you please explain to me what is happening?<br>> >>>> > > > ><br>> >>>> > > > > Thanks.<br>> >>>> > > > ><br>> >>>> > > > > Darrell<br>> >>>> <br>> -- <br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. 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