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?
-Justin
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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