[gmx-users] Re: Turning off electrostatics between groups using custom tables?

Smitty mds322 at drexel.edu
Fri Aug 31 18:50:03 CEST 2012

> While for the protein-protein or ion-group ion-group interactions I provide
> just the standard 6-12 table. The problem comes that when I run using my
> modified table, the system will run but gradually explodes. I note that
> when
> I look back at my output from grompp I find a warning concerning eplison
> and
> sigma being used instead of C6 and C12,

>>Ignoring warnings is a great way to waste time, and if you can't provide 
>>specific details of what it was, you're unlikely to get specific help.

The warning is as follows: 

WARNING 1 [file pep_ion.top, line 1218]:
Using sigma/epsilon based combination rules with user supplied potential
function may produce unwanted results. I've looked into this on the mailing
list, but it appears that so long as the forces are what I expect them to
using the standard tables, I should be able to ignore this warning.
Hopefully I have not misread the previous threads.

>   but if I swap my custom table for
> the sample 6-12 table (keeping the first two columns not zero) the system
> doesn't explode and has dynamics similar to previous simulations making
> use
> the built-in table generation. Any ideas on where I am going wrong?

>>Can't tell. What's the "ion group"? Does it even get close to Protein?

The "ion group" is a set of 50 dissociated ions (25 K+, 25 Cl-). The ions
under standard simulation conditions (non-custom interaction table) rarely
have K+ or Cl- atoms coming within 0.5 angstroms of any atom of the protein
group; but they do still happen. If it helps my .mdp file for the simulation
is attached.  http://gromacs.5086.n6.nabble.com/file/n5000727/md.mdp md.mdp 

Thanks again, hope this clears up my question.


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