[gmx-users] Tables with forcefield

ms devicerandom at gmail.com
Sat Sep 25 01:07:11 CEST 2010


Clarification: I may not be able to help you directly but I can suggest 
you which information you should perhaps give us to enable people more 
knowledgeable than me to help.

On 24/09/10 17:33, Sai Pooja wrote:
>> 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?

I am not "suggesting": I am only saying what I am doing :)

>> 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.

This is absolutely doable -I do it everyday, in fact. So, don't despair. :)

Now, it seems that you talked about a problem with convergence of the 
SETTLE algorithm. I know little about it, but, couldn't it simply be 
that your tables are "wrong" (that is, they don't play well with 
algorithms?) What is their shape, actually, and on which 
atomtypes/groups are you applying your table? What is the forcefield you 
are using along with the table?


More information about the gromacs.org_gmx-users mailing list