On 1/09/2012 1:14 AM, Smitty wrote:
Hi,
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,
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.
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?
Mark
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!
-Smitty
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