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.
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.