[gmx-users] Re: Turning off electrostatics between groups using custom tables?
Smitty
mds322 at drexel.edu
Sun Sep 2 20:47:13 CEST 2012
> 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.
> 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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Thanks mark, I have since gone back and modified the .mdp file after
re-reading the tutorial and manual and have come up with the new attached
.mdp file ( http://gromacs.5086.n6.nabble.com/file/n5000746/md.mdp md.mdp ,
which I think removes the problems you highlighted in 1) and 3).
I no longer have an exploding system; however, when I run g_energy on the
output .edr file from a short run (looking at the K+ and protein energy
groups) I get the following output:
Energy Average RMSD Fluct. Drift
Tot-Drift
-------------------------------------------------------------------------------
Coul-SR:K+-K+ 551.07 208.162 89.6287 0.69831
650.828
LJ-SR:K+-K+ 1.43168 0.794798 0.668453 0.00159813
1.48946
Coul-14:K+-K+ 0 0 0 0
0
LJ-14:K+-K+ 0 0 0 0
0
Coul-SR:K+-Protein -6994.99 1978.5 1003.44 -6.33779
-5906.85
LJ-SR:K+-Protein 52.3447 13.7398 11.2697 0.0292135
27.2271
Coul-14:K+-Protein 0 0 0 0
0
LJ-14:K+-Protein 0 0 0 0
0
Coul-SR:Protein-Protein -246.639 43.9503 30.246 0.11852
110.461
LJ-SR:Protein-Protein -81.9209 10.2086 9.29929 0.0156543
14.5899
Coul-14:Protein-Protein 1477.91 19.7693 16.2154 -0.0420325
-39.1745
LJ-14:Protein-Protein 158.219 11.1455 10.5729 -0.0131077
-12.2164
Which is closer to what I am going for, but I would expect that the
Coul-14/LJ-14 K+-K+ would not be zero. Any ideas on what I am still not
doing correct? Thanks for all the help.
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