[gmx-users] Non-bonded interaction

[Mark Abraham]

Hi,

Please check out the equations and non-bonded combination rules in chapter
4 of the manual, and the units in chapter 2.

Mark


On Sat, May 31, 2014 at 2:43 PM, 라지브간디 <rajiv at kaist.ac.kr> wrote:

> Dear justin,
>
> Could tell me how do I convert those non-bonded values between CHARMM and
> gromos431 ?
>
> I am unaware of this conversion.
>
> Thanks in advance.
>
> On 5/30/14, 11:51 AM, ????? wrote:
> >
> > Dear justin,
> >
> > Thank your for your clear answer.
> >
> > The parameters are specifically written for CHARMM force field based on
> the experimental results.
> >
> > Particularly, charges and non-bonded interaction values for ligand
> molecule of CO ( Carbon Monoxide) in Myoglobin are written in literature.
> >
> > Since Gromos 43a1 has parameter for heme with CO, therefore I asked you
> " Is that possible to use only this CO ligand charges and non-bonded values
> derive
> >
> > d from experimental and written in CHARMM ff ?.
> >
> > In other case, shall I use this CHARMM ff values for CO in CHARMM27/36
> provided by groamcs without doing any conversion ?
> >
>
> Yes, you need to convert the units (CHARMM and Gromacs use different
> conventions), but otherwise those parameters can be used directly with
> CHARMM27
> or CHARMM36.
>
> -Justin
>
> > Thanks in advance.
> >
> > On 5/29/14, 10:13 PM, ????? wrote:
> >> Dear Justin,
> >>
> >> Thanks for your
> >> reply.
> >>
> >> I am not mixing up the parameter here.
> >> What i am trying to do here
> >> In order to reproduce the dipole moments of the CO, I have to
> >> follow up the specific charges and non-bonded interaction values
> specified in
> >> literature in CHARMM format ( For C atom, charge -0.75, ?=0.0262
> >> & ? = 3.83) ( For O atom, charge -0.85, ?=0.0262 & ? =
> >> 3.83).
> >
> > "CHARMM format" and "CHARMM force field" are different, so what is the
> origin of
> > those parameters? Were they developed specifically for CHARMM or some
> other
> > force field? If these parameters were not specifically designed to be
> > consistent within Gromos96 43A1, my original point stands - they cannot
> be
> > combined with a force field for which they were not self-consistently
> derived.
> >
> >> Could you tell how it can be done? If i cant use them in
> >> gromos43a1 ff, possible to use in charmm27 provided by gromacs package?
> or it
> >> does need any conversion to use in gromacs-charmm27 ff?
> >>
> >
> > Both CHARMM27 and CHARMM36 are fully supported by Gromacs.
> >
> > -Justin
>
> --
> 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-request at gromacs.org.
>