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Hi,<br><br>I am 99.99% sure that there is no problem with COM motion removal in Gromacs.<br>Could you post your mdp parameters?<br><br>Berk<br><br>> From: x.periole@rug.nl<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] Martini simulation problem in recentering trajectory so that the bilayer is at the center<br>> Date: Wed, 2 Sep 2009 16:04:39 +0200<br>> <br>> <br>> I am not sure how to fix the trajectory that has drifted ...<br>> <br>> But if your bilayer drifts even if you use a removal of the COM for <br>> the water and<br>> bilayer separately that means there is problem in the code! And this <br>> should be<br>> fixed.<br>> <br>> XAvier.<br>> <br>> On Sep 2, 2009, at 3:36 PM, maria goranovic wrote:<br>> <br>> > Dear Experts<br>> ><br>> > I had posted this earlier, but the problem was not solved by earlier <br>> > suggestions. So am posting again.<br>> ><br>> > I am simulating a POPC bilayer using MARTINI. The simulation ran <br>> > fine, but the bilayer drifted towards the edge of the box along the <br>> > bilayer normal, and eventually some of the atoms crossed the box <br>> > boundaries. In some cases, entire lipid molecules crossed the box <br>> > boundaries. I tried to recenter the trajectory, so that the lipid <br>> > bilayer would be at the center of the box at all times. But for some <br>> > reason, this does not seem to work? I have tried simulations using a <br>> > single comm_group for the entire system, as well as separate ones <br>> > for the lipid and water, but the same problem appears in either case.<br>> ><br>> > Typically, for all-atom bilayers, the following set of commands <br>> > works to correct the drift:<br>> ><br>> > #### first convert original trajectory to a temp. xtc ###<br>> > echo 3 0 | trjconv -s *tpr -f original.xtc -o temp.xtc -center - <br>> > boxcenter zero -pbc mol -n popc.ndx<br>> > #### then convert temp.xtc to the final trajecory ###<br>> > echo 3 0 | trjconv -s k*tpr -f temp.xtc -o final.xtc -center - <br>> > boxcenter zero -pbc mol -n popc.ndx<br>> ><br>> > where groups 3 and 0 are the lipid and the whole system <br>> > respectively, and final.xtc is my final trajectory.<br>> ><br>> > However, this does not work for the MARTINI systems. Looking at the <br>> > final trajectory in VMD, the bilayer is either at the center of the <br>> > box, or it is split at the box edges, with each monomer being in <br>> > different leaflets.<br>> ><br>> > If I plot the center of mass motion of the entire system in the <br>> > original trajectory .. the system seems to drift by ~ 2-3 angstroms <br>> > in one direction. As a result, water center of mass drifts in the <br>> > opposite direction (because of PBC).<br>> ><br>> > Are there any suggestions to sort this out? One option is to write <br>> > the entire trajectory to .gro files, recenter all of them (depending <br>> > upon whether the bilayer is in the center or is split at the box <br>> > edge), and concatenate the gro files again.but this is tedious, even <br>> > if scripted.<br>> ><br>> > Please let me know if i can provide any additional info ?<br>> ><br>> > -- <br>> > Maria G.<br>> > Technical University of Denmark<br>> > Copenhagen<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>> _______________________________________________<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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