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

Justin A. Lemkul jalemkul at vt.edu
Wed Jul 22 19:10:16 CEST 2009

Kirill Bessonov wrote:
> 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?

Depending on how many atoms you have in your system and how often you are saving 
coordinates and velocities, it could be.  If you're using my .mdp files from the 
tutorial, note that you should probably never use nstxout = 100 for a 10 ns 
equilibration :)  I use small values for short equilibrations so I can catch 
enough frames in case there's a crash.

> 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?

Yes, the water goes one way, the bilayer goes the other way, and overall there 
is no COM motion.  I believe the problems manifest themselves if you are trying 
to calculate diffusion coefficients and perhaps other parameters.

> 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.

As specified in my tutorial, you have to run InflateGRO *many* times to return 
the box to normal dimensions.  I believe I used 25 or 26 iterations (scaling by 
0.95 each time, followed by EM) to return my system to a reasonable area per lipid.


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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


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