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: 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. 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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