[gmx-users] Martini simulation problem in recentering trajectory so that the bilayer is at the center

[Berk Hess]

Hi,

I am 99.99% sure that there is no problem with COM motion removal in Gromacs.
Could you post your mdp parameters?

Berk

> From: x.periole at rug.nl
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Martini simulation problem in recentering trajectory	so that the bilayer is at the center
> Date: Wed, 2 Sep 2009 16:04:39 +0200
> 
> 
> I am not sure how to fix the trajectory that has drifted ...
> 
> But if your bilayer drifts even if you use a removal of the COM for  
> the water and
> bilayer separately that means there is problem in the code! And this  
> should be
> fixed.
> 
> XAvier.
> 
> On Sep 2, 2009, at 3:36 PM, maria goranovic wrote:
> 
> > Dear Experts
> >
> > I had posted this earlier, but the problem was not solved by earlier  
> > suggestions. So am posting again.
> >
> > I am simulating a POPC bilayer using MARTINI. The simulation ran  
> > fine, but the bilayer drifted towards the edge of the box along the  
> > bilayer normal, and eventually some of the atoms crossed the box  
> > boundaries. In some cases, entire lipid molecules crossed the box  
> > boundaries. I tried to recenter the trajectory, so that the lipid  
> > bilayer would be at the center of the box at all times. But for some  
> > reason, this does not seem to work? I have tried simulations using a  
> > single comm_group for the entire system, as well as separate ones  
> > for the lipid and water, but the same problem appears in either case.
> >
> > Typically, for all-atom bilayers, the following set of commands  
> > works to correct the drift:
> >
> > #### first convert original trajectory to a temp. xtc ###
> > echo  3 0 | trjconv -s *tpr -f original.xtc -o temp.xtc -center - 
> > boxcenter zero -pbc mol -n popc.ndx
> > #### then convert temp.xtc to the final trajecory ###
> > echo  3 0 | trjconv -s k*tpr -f temp.xtc -o final.xtc  -center - 
> > boxcenter zero  -pbc mol -n popc.ndx
> >
> > where groups 3 and 0 are the lipid and the whole system  
> > respectively, and final.xtc is my final trajectory.
> >
> > However, this does not work for the MARTINI systems. Looking at the  
> > final trajectory in VMD, the bilayer is either at the center of the  
> > box, or it is split at the box edges, with each monomer being in  
> > different leaflets.
> >
> > If I plot the center of mass motion of the entire system in the  
> > original trajectory .. the system seems to drift by ~ 2-3 angstroms  
> > in one direction. As a result, water center of mass drifts in the  
> > opposite direction (because of PBC).
> >
> > Are there any suggestions to sort this out? One option is  to write  
> > the entire trajectory to .gro files, recenter all of them (depending  
> > upon whether the bilayer is in the center or is split at the box  
> > edge), and concatenate the gro files again.but this is tedious, even  
> > if scripted.
> >
> > Please let me know if i can provide any additional info ?
> >
> > -- 
> > Maria G.
> > Technical University of Denmark
> > Copenhagen
> > _______________________________________________
> > gmx-users mailing list    gmx-users at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before  
> > posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> 
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

_________________________________________________________________
Express yourself instantly with MSN Messenger! Download today it's FREE!
http://messenger.msn.click-url.com/go/onm00200471ave/direct/01/
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090902/d24e5c58/attachment.html>