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

intra\sa175950 stephane.abel at cea.fr
Thu Sep 1 18:12:39 CEST 2011

Hi Chris, 

Sorry to repost the same question, but I have really tested your method the
last few weeks. My question about the gen-pairs directive come from the fact
that I have read a message from you 


Where you detailed how to use the Berger and OPLS force fields together in
the same system. By reading carefully the meaning of the gen-pairs
directive, I found several errors in my force field. 

BYW in your previous message 


In the step 3, I think there is a typo, it is "values/10" instead of
"values/12". Am I right?

Thank you again 



Dear Stephane:

We discussed this in April:


At that time I also provided a method for you to verify your files  
(and the method in general).

It is possible for you to answer your gen-pairs question by looking  
into the manual and reading about pairs, gen-pairs, and pairtypes. I  
think that this is one case where you would benefit more from fully  
understanding how these parts work than from a direct answer to your  

If you are having problems, please provide a whole bunch more  
information on the problems that you are seeing. If, on the other  
hand, you are just looking for somebody other than me to comment on  
the accuracy of the April post, then that is perfectly fine with me,  
but you should state that.


-- original message --

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

#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"


Thank you for your help


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