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

Kirill Bessonov kbessonov at gmail.com
Fri Jul 17 18:22:09 CEST 2009

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 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.

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

I have attached images, also if the didn't come through I have included
lincs to them:

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