[gmx-users] Tables with forcefield

Sai Pooja saipooja at gmail.com
Fri Sep 24 18:33:37 CEST 2010


Clarifications inline...
On Wed, Sep 22, 2010 at 2:01 PM, ms <devicerandom at gmail.com> 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


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