On 6/21/17 10:39 AM, gozde ergin wrote:
Hi MArk,
Thanks for the respond. I understood that point however I still do not get
which sigma to change.
I the paper JCTC 2017, Miller et. al. they have mentioned that they increase
the for nitrogen–carboxylate oxygen interactions in OPLSAA.
However there are two sigma in oplsaa.ff/ffnonbonded.itp one for amino notrogen
and one for carboxylate oxygen.
sigma epsilon
opls_287 N3 7 14.00670 -0.300 A 3.25000e-01 7.11280e-01
opls_272 O2 8 15.99940 -0.800 A 2.96000e-01 8.78640e-01
Which one defines the amino nitrogen–carboxylate oxygen interactions?
Which sigma should I change?
What people are doing more and more is introducing pair-specific parameters to
override the combination rule values. That's likely what is being referred to.
OPLS-AA by default does not use pair-specific LJ interactions, hence why you
find no [nonbond_params] in ffnonbonded.itp. The same is true of AMBER. CHARMM
uses some (also called NBFIX in the literature), while GROMOS uses a ton of these.
To override the LJ combination rules, add a [nonbond_params] directive with the
published parameters, which refer to an *interaction*, not an atom type.
-Justin
Thanks
On 21 Jun 2017, at 16:21, Mark Abraham <mark.j.abra...@gmail.com> wrote:
Hi,
Different force fields work differently and thus are implemented
differently. Look at oplsaa.ff/ffnonbonded.itp and you will see that sigma
is a property of the atomtype
Mark
On Wed, Jun 21, 2017 at 4:16 PM gozde ergin <gozdeeer...@gmail.com> wrote:
Dear users,
I am trying to change the sigma value of amino nitrogen–carboxylate oxygen
interactions in OPLSAA in GROMACS.
However I have difficulties to understand which parameter i should change
in ffnonbonded.itp file?
I am looking something like [ nonbond_params ] section however it is not
exist in ffnonbonded.itp?
Any help would be appreciated.
Thanks in advance.
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Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
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