[gmx-users] Peptide - DMPC membrane simulations -> Unstable system

Kirill Bessonov kbessonov at gmail.com
Wed Jul 22 18:18:40 CEST 2009

Hi Justin,

So after struggling through ... I have confirmed that the error was due to
Gromacs version incompatibility. Now my simulation is past problematic step
and continues running without any error.

Also I am following your advice and also doing the same simulation but with
two equilibration steps as per your tutorial. The pressure equilibration
step had generated 7Gb *.trr file, is this normal for 10ns equilibration?

I have used mdp files from tutorial too. I have question about COM (center
of mass) parameters. What happens if we forget about them and do not do the
grouping of Solvent+Na+ + Cl- and Protein+DMPC, what could happen?
The layer will slide past each other, or what?

And one more question about your tutuorial and my previous experiences:
Also when I was running InflateGRO my box size incread 4x, so it became
huge, 25x25x25, and after compression by 0.95 factor is was around 22x22x22.
Therefore I have used the box that we had in the lab already. Is this
normal, because visiaully lipids are too spaced out and that's why water
enters btwn them when you solvate, to the poin that I wrote C++ program that
removes water from lipid bilayer.
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