[gmx-users] [Fwd: How simulate two peptides in a box?]

[Mark Abraham]

> 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
> topology
> file. I have seen my topology file and the related .itp files also but i
> did
> 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
> #endif
>
> ; 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
the problem.

Mark