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

Justin A. Lemkul jalemkul at vt.edu
Wed Sep 2 16:04:38 CEST 2009

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.

The -center option will place the center of mass of the group in the center of 
the box, so having to the two leaflets at the "top" and "bottom" of the box 
still satisfies this criterion.  The better approach is to choose a single 
lipid, or even a tail atom of one lipid, as the group to be centered.

> 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).

How did you specify COM motion removal in your .mdp file?


> 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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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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