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
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