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<br><br>> To: gmx-users@gromacs.org<br>> Date: Thu, 26 Nov 2009 19:43:00 +0000<br>> From: darrellk@ece.ubc.ca<br>> Subject: [gmx-users] Unexpected behavior of g_msd<br>> <br>> <br>> Hi Berk,<br>> I am thinking that you mean that MSD is a function of the time<br>> differences and the number of time differences. In other words, if the<br>> simulation is too short, then GROMACS would not have enough time<br>> differences to accurately calculate a diffusion constant since the slope<br>> of the msd versus time within these time intervals would vary too much.<br>> Thus, I thought that, in order to get an accurate measurement of<br>> diffusion, it was necessary to run the simulation for a long enough<br>> period of time to get into a region where there is a linear relationship<br>> between msd & time so that the regression fit is improved. Is this<br>> correct?<br><br>That's correct.<br><br>> <br>> In the paper "The Working Man’s Guide to Obtaining Self Diffusion<br>> Coefficients from Molecular Dynamics Simulations", they indicate that a<br>> simulation time of approximately 2 ns is appropriate for gas phase<br>> simulations and that the section of time interval used for calculating<br>> the diffusion constant be the linear region near towards the end of the<br>> simulation.<br><br>This will depend VERY much on the type of system and the state point.<br><br>Berk<br><br>> <br>> Thanks.<br>> <br>> Darrell<br>> <br>> >Date: Thu, 26 Nov 2009 11:34:02 +0100<br>> >From: Berk Hess <gmx3@hotmail.com><br>> >Subject: RE: [gmx-users] Unexpected behavior of g_msd<br>> >To: Discussion list for GROMACS users <gmx-users@gromacs.org><br>> >Message-ID: <COL113-W20188A074F24AF04DD1C638E9B0@phx.gbl><br>> >Content-Type: text/plain; charset="iso-8859-1"<br>> ><br>> ><br>> >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>> 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 />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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