On 1/09/2012 2:50 AM, Smitty wrote:
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
1) That .mdp applies different tables to K-K, protein-protein and all
other interactions, which isn't what you've said you've done.
2) You should follow the advice here
http://www.gromacs.org/Documentation/Terminology/Thermostats
3) Your life will be simpler if you use energygrp_table only for the
group-group interactions you want to change, and leave the default
interactions normal. It will also be faster, because using tabulated
interactions is much slower than the normal ones.
Mark
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