[gmx-users] Use different fudgeLJ and fudgeQQ values in simulations with the AMBER force field

intra\sa175950 stephane.abel at cea.fr
Thu Aug 11 16:16:44 CEST 2011

Dear All,


Few years ago, C. Neale (thanks to him!) posted in the GROMACS mailing list
a very useful tutorial [1] to scale the Coulombic 1-4 interactions when we
combine forcefields with different fudgeLJ and fudgeQQ values. I am trying
to apply this trick to a system containing a peptide and a micelle simulated
with AMBER99SB-ILDN and GLYCAM force fields, respectively (see my previous
message [2]). 


I have followed all the steps described in [2] and computed the sigma_ij and
epsilon_ij values for the peptide and the micelle with comb_rules 2 (i.e.
sigma_ij=1/2(sigma_i+sigma_j) and epsilon_ij=sqrt(epsilon_i*epsilon_j). The
epsilon_i and sigma_i are taken from the [ atomtypes ] section in the
ffnonbonded.itp file


However, in the step 3 in [2], it is said that the peptide the pair
interaction values (i.e. epsilon) should be divided by 10 and these
"values/12" include in the pairtypes section. I suspect a typo here. Indeed,
if I set the general fudgeLJ and fudgeQQ to 1.0 and 0.1666666, I should have
a ratio of 10 (for (0.83333/(0.166666)))*1/2 for epsilon_ij and not "12". Am
I right?


To test the changes, I have performed three nsteps=0 runs in NVT ensemble
for a simple system (1 peptide and 1 glycolipid solvated in water) with the
initial and modified and non-modified nonbonded parameters:


1- With ffnonbbonded.itp file non-modified with fudgeLJ=0.5 and
fudgeQQ=0.83333   --- > peptide

2- With ffnonbbonded.itp file non-modified with fudgeLJ=1.0 and fudgeQQ=1.0
--- >  micelle

3- With ffnonbbonded.itp file modified with fudgeLJ=1.0 and
fudgeQQ=0.1666666  --- >  all


and compared the *.trr files obtained from these the three runs. 


The only differences I found are, indeed, in the force section of the *.trr
files for atoms involved in the modified pair section. To be sure that my
modifications are corrects, I would like to obtain the individual pair
energy values of the micelle and the peptide. How to obtain this values?   


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

[2] http://lists.gromacs.org/pipermail/gmx-users/2011-April/060839.html


Thank you again for your help and advices.  



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