On 12/08/2011 12:16 AM, intra\sa175950 wrote:
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
Using mdrun -rerun allows you to compare more than one configuration in
a run, and avoid any issues associated with bond constraints and
neighbour lists.
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?
Use grompp -pp, and selectively zero out charges and/or VDW parameters
for appropriate [moleculetypes] in the reruns.
Mark
[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.
Stephane
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