[gmx-users] [Fwd: How simulate two peptides in a box?]
mark.abraham at anu.edu.au
Wed Jul 4 09:16:39 CEST 2007
> Thanks Mark for your advice
> I tried to run the simulation even by removing all the restraints as you
> told but the same problem was coming.
> In your second reply you asked me to check the topology file. I have a
> doubt in that, actually what are the things i should look at in the
> file. I have seen my topology file and the related .itp files also but i
> not find anything unusual in that.
> Following are the contents of my Topology file:
> ; Include forcefield parameters
> #include "ffG43a1.itp"
> ; Include chain topologies
> #include "aquapomut_grom_A.itp"
> #include "aquapomut_grom_B.itp"
> ; Include water topology
> #include "spce.itp"
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ; i funct fcx fcy fcz
> 1 1 1000 1000 1000
> ; Include generic topology for ions
> #include "ions.itp"
> [ system ]
> ; Name
> Protein in water
> [ molecules ]
> ; Compound #mols
> Protein_A 1
> Protein_B 1
> SOL 71
> CL- 6
> SOL 14825
Two regions of SOL doesn't sound like a good idea, but I won't swear it's
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