[gmx-users] Re:GROMACS WINDOWS

Ing. Vojtěch Spiwok Vojtech.Spiwok at vscht.cz
Tue Sep 16 12:17:00 CEST 2003

> Hope someone can offer some suggestions.
> I'm running gromacs under windows (xp).
> I've run done a few runs with a protein and it works fine.
> Now when I try a run with an oligomer, mdrun crashes and closes.
> I setup the water box and am running the energy 
> minimisation/dynamics run on the water molecules, and I get a 
> crash message from windows saying mdrun crashed!
> Any ideas?
> Many thanks
> Raj Badhan
I have done some oligomer dynamics on WinXP and
it worked. Is the dimer in input pdb writen as two
monomers A and B each starting from residue 1?
If not, try it. A and B must be in the column between
residue number and residue type in PDB file. Otherwise,
you can try to renumber residues constitutively. Then
beware of correct topology on the last residue of the
first monomer and first residue of the second monomer. 

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