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

Justin A. Lemkul jalemkul at vt.edu
Fri Jul 17 18:32:49 CEST 2009

Kirill Bessonov wrote:
> Hello again,
> Thanks for quick replies!  I've tried to see what happens if I put 
> peptide in water and sure enough it failed (uses gromacs 4.0). But when 

A simple peptide in water fails?  Again, it would be helpful to see your .mdp 
file to make sure it is sound.

> I run it on machine that I have created the *.tpr file it runs no 
> problem already 5000 steps and the machine uses gromacs 4.0.5.
> How could it be possible, after all the Gromacs versions are very similar.

Several bugs have been fixed since the release of 4.0.  I got random, sporadic 
LINCS crashes with some of my membrane systems from a tricky little bug related 
to DD.  Berk fixed it prior to the release of version 4.0.2.  It is best to 
always use the latest version for running simulations.

> To solavate I have used genbox -cp protein.gro -cs DMPCbox(bilayer with 
> water ontop) -box [dimensions] -

If the peptide and DMPC are making contacts, they could be generating clashes 
that lead to the explosion.  Your EM looked pretty good, but without seeing your 
.mdp file for what you're trying to do, it's difficult to say what the problem 
might be.

> I have attached images, also if the didn't come through I have included 
> lincs to them:
> http://kbessonov.googlepages.com/DMPC_cage.gif
> http://kbessonov.googlepages.com/A141_simulSys.png
> http://kbessonov.googlepages.com/A141inDMPC.GIF
> After running simulation for couple of hours I have discovered that DMPC 
> molecules are flying apart, showing as some rays in a form of a cage as 
> you see form the DMPC pic.

These "cages" are just visualization artefacts.

> What can I do to prevent this artifact, is there trjconv command to ma 
> ke corrections so I do not see this strange artifact?

trjconv -pbc mol -ur compact usually works for me, for most systems (membrane or 
not).  Play around with the -pbc options if for some reason it doesn't work out.


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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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