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

[Erik Marklund]

2 sep 2012 kl. 20.47 skrev Smitty:

> 
> 
>> 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.
> 

Why would you have 1-4 interactions for monoatomic species? Or between different molecules for that matter?

> 
> 
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-----------------------------------------------
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 6688        fax: +46 18 511 755
erikm at xray.bmc.uu.se
http://www2.icm.uu.se/molbio/elflab/index.html