[gmx-users] half double pair list method in GROMACS

[intra\sa175950]

Dear All, 

 

I try to apply the half double pair list method for a system containing a
glycolipid surfactant and a peptide modeled with the GLYCAM and AMBER99SB
force field. Briefly what I did : 

 

1- I have changed the  forcefield.itp like this 

 

[ defaults ]

; gen_pairs set explicitly ---> gen-pairs = "no"

; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ

;1               2               yes             0.5     0.8333 ---> for
AMBER99SB only

1               2                no             1.0     0.16666666666666 ---
> for both GLYCAM et AMBER99SB

;1               2                yes              1.0     1.0 --> for
GLYCAM only

 

#include "ffnonbonded_mod.itp"

#include "ffbonded.itp"

 

2- For the surfactant, I have calculated the pair-types interactions
manually with the comb-rule = 2 and divided the values /6 and added these
values in [pairtypes] section in the ffnonbonded_mod.itp files

 

3- For the peptide, I have calculated the pair-types interactions manually
comb-rule = 2 and divided the values /10 and added these values in
[pairtypes] section in the ffnonbonded_mod.itp files. 

 

4- In the surfactant topology file I have repeated 6 times the [pairs]
directives 0.166666*6 ~=10

 

5 - In the peptide topology file I have repeated 5 times the [pairs]
directives 0.166666*5 ~= 0.8333

 

Is it correct ?

 

However I have a little doubt about "gen-pairs" directive should I have set
it to "no" or "yes". in a previous message with a similar problem, the gen
directive was set "yes" 

 

http://lists.gromacs.org/pipermail/gmx-users/2006-September/023761.html

 

Thank you for your help

 

Stephane

 

 

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