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

XAvier Periole x.periole at rug.nl
Wed Sep 2 16:04:39 CEST 2009

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


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
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