[gmx-users] Problem with COM movement
Tomy van Batis
tomyvanbatis at gmail.com
Tue Jan 11 12:28:04 CET 2011
I have the following system:
Two substrates (which are FCC lattices consisting of LJ particles) in a
distance of 50nm and between these substrates I put completely stretched
polymer chains. The substrates are parallel to xy plane and the chains are
vertical. The length of the stretched chains is 30 nm and I put them in the
middle, so the distance of the each substrate to be 10nm. The interaction
between the substrates and the polymers is repulsive and it’s the same for
I want my substrates to be stable during the simulation, but to be able also
to move under compression (in the z axis).
For that purpose in my .mdp file I define the following:
*nstcomm = 1*
*comm-grps = ZZZ **,where ZZZ is the name of the residue of
I have 2 problems:
1) At the beginning, I run NVT for 20ns and the chains are moving UP
during the simulation.
Since my system is completely symmetric, I would expect to have symmetric
movement of the chains, i.e. symmetric density profile.
2) In my .log file the following message appears:
*Large VCM(group rest): 0.00000, -0.00000, 0.00001,
It doesn’t appear as an error message, but it appears thousand times in my
log file. I had a look in the mailing list about that, but I did not find a
Can anyone help me?
I also have one question:
When I remove that COM motion of one residue, i.e. from the ZZZ (by adding
comm grps: ZZZ in my mdp file), what happening with the COM motion of the
rest of the system?
I hope I was clear!
Thanks in advance, Chrysostomos
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