[gmx-users] mixed 1-4 scaling factor

Mark Abraham mark.j.abraham at gmail.com
Fri May 5 14:40:15 CEST 2017


As you can see in the documentation of the topology file format in chapter
5 of the reference manual, whether intra-molecular "pair" interactions for,
say, 1-4 interactions have parameters generated from the normal non-bonded
interactions (perhaps via scaling), or not is a property of the force
field. So if these parameter sets are intended to be mixed (GLYCAM website
is broken, so I can't tell), then you'll need to make an appropriate choice
in the .top for one parameter set, and specify explicit [pairs] with
parameters, (or [pairtypes]) for the other kinds of parameters.

Test first on a simple system, e.g. that the energy of a peptide by itself,
and a carbohydrate by itself add up to that of the two together (spaced far
enough apart).

Please report back what you find, so future users like you might be able to
find it!


On Wed, May 3, 2017 at 12:01 AM Qinghua Liao <scorpio.liao at gmail.com> wrote:

> Hello,
> I want to simulate a system using Amber and Glycam force fields together
> with gromacs,  I am wondering whether
> a scheme of mixed 1-4 scaling factors is available with Gromacs.
> I searched the mailing list, and I found this post which no one responded:
> https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2014-June/090120.html
> And I also found this post, but it is not very clear.
> https://www.mail-archive.com/gromacs.org_gmx-users@maillist.sys.kth.se/msg03639.html
> Could someone give me some tips on the problem? Thanks very much!
> All the best,
> Qinghua
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