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

maria goranovic mariagoranovic at gmail.com
Wed Sep 2 15:36:47 CEST 2009

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
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