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

Smitty mds322 at drexel.edu
Fri Aug 31 17:14:26 CEST 2012

I've been trying to turn off the electrostatic interaction between two
groups (an ion-group and protein) by following the tutorial on custom table
generation, but have seemed to have hit a road block.

Looking at the structure of the sample 6-12 table provided in the topology
directory, I constructed my table.xvg for interactions between the two
groups to be the following:

#r coulomb coulomb-force 1/r^6 6/ r^7 1/12 12/r^13 
0    0           0                   0         0       0       0  
0.04 0          0                 -2.4414062500e+08 -3.6621093750e+10  
5.9604644775e+16 1.7881393433e+19

and so on.  Noting that the second and third columns are defined as zero for
all steps, while the columns related to LJ are left unchanged.

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, 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? 

Here are the other specs for the simulations:
Gromacs 4.0.5, OPLS/AA, berendsen pressure/temperature coupling: tau_p =0.5,
tau_t=0.1, simulation temperature 283.

Any help is much appreciated!

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