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

[ABEL Stephane 175950]

Chris,

Thank you for your confirmation. I did the changes. I am currently doing some tests, I will send you a feedback about the results off-list (if you want) shortly.

A bientôt 

Stéphane
________________________________________



Message: 1
Date: Thu, 01 Sep 2011 14:38:53 -0400
From: chris.neale at utoronto.ca
Subject: [gmx-users] Half double pair list method in GROMACS
To: gmx-users at gromacs.org
Message-ID: <20110901143853.537ln0dj94w4wc4c at webmail.utoronto.ca>
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It's a typo, but it's in the discussion and not in the "do this" part
of the method so I decided not to mention it. I don't see another
question in this post, so I hope that you have figured things out.
Note that I have never tested the exact implementation that I
suggested in that April email. It seems like it should work just fine,
but it is numerically different than the OPLS/Berger combination so
there is no way to be sure until you check the energies as I
suggested. I'd be interested to have you report back on the energy
matching once you have done the tests.

Good luck,
Chris.

-- original message --

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

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

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

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

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

Thank you again

Stephane



Dear Stephane:

We discussed this in April:

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

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
question.

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.

Chris.


-- 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
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