Hi, Clarifications inline... On Wed, Sep 22, 2010 at 2:01 PM, ms <[email protected]> wrote:
> On 21/09/10 20:45, Sai Pooja wrote: > >> I wanted to change the interactions between the Protein and Solvent so I >> tried using tables with the potential function scaled by a constant value. >> I >> wanted to use this in combination with forcefield parameters (charmm). I >> changed the combination rule in the forcefield.itp file from '2' to '1' >> since tables use C6 and C12 values. To test the system I started with >> default tables. >> >> When I run grompp, it generates the .tpr file successfully but in the md >> simulation using mdrun, settle does not converge. It does not converge for >> 1 >> water molecule. >> >> If I go back to the combination rule '2' in the forcefield.itp file, I get >> a >> warning that using combination rule 2 with tables may generate error. >> >> With combination rule '2' and cutoff for both vanderwaals and coulombtype, >> i >> face no problem. >> > > I use combination rule 1; but I also define all tabulated interactions for > all possible *pairs* under the [ nonbond_params ] section, so the > combination rule actually doesn't matter much. Are you suggesting that I can change the combination rule in the forcefield.itp file but I must also supply a table for pairs using -tablep option for this to work? > > > Does this mean that one cannot use tables with forcefield parameters? >> > Clarification: I want to use forcefield parameters with user defined tables i.e. I want to use sigma and epsilon values generated by pdb2gmx along with a user-defined modified potential energy function using tables. > > I am not sure of understanding with question -can you clarify? > > Massimo > Pooja > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- Quaerendo Invenietis-Seek and you shall discover.
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