[gmx-users] Tables with forcefield
saipooja at gmail.com
Mon Sep 27 22:18:21 CEST 2010
I am using the standard 6-12 tables available with the gromacs package. For
-table and -tablep options to start with.
I want to understand 1 thing. The forcefield files and the topology file
specifies sigma and epsilon parameters. If I change the combination rule to
1 in the forcefield.itp file, and use tables, how does gromacs convert the
sigma, epsilon values in the topology file to C6 and C12?
On Fri, Sep 24, 2010 at 7:07 PM, ms <devicerandom at gmail.com> wrote:
> 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
>> 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
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