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Hi,<br><br>You don't need trjconv, g_msd has options -b and -e.<br>But the regression is obviously done on the time differences and not on<br>the frame times. MSD is a function of a time difference, not of simulation time.<br><br>Berk<br><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>> > -----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>> > > > Dear GROMACS-ites,<br>> > > > I am a little confused by the behavior of g_msd. I have a trr file<br>> > with data<br>> > > > points from t=0 to t=100 ps and thought that the following command<br>> > would<br>> > > > perform a regression for the data points between t=60 ps and t=100<br>> > ps to<br>> > > > determine the diffision constant of the ammonia gas in the<br>> > simualtion:<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>> > and<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<br>> > posting!<br>> > Please don't post (un)subscribe requests to the list. Use the<br>> > www interface or send it to gmx-users-request@gromacs.org.<br>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<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. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br> <br /><hr />New Windows 7: Simplify what you do everyday. <a href='http://windows.microsoft.com/shop' target='_new'>Find the right PC for you.</a></body>
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