[gmx-users] Re: different sets of fudgeQQ and fudgeLJ

[Oliver Grant]

Hi Yun,

Mixed 1-4 scaling of AMBER and GLYCAM requires a trick originally designed
for including berger lipids and the OPLS forcefield. I think* the original
idea came from Chris Neale and I think there is a paper in detailed in there
you should cite. It was recently explained on the GMX list how to adapt it
to GLYCAM and AMBER. See here:
http://www.mail-archive.com/gmx-users@gromacs.org/msg43703.html

That thread also has links to Chris Neale's original posts. I suggest
reading his posts as they explain how it works very well. You will be able
to do mixed scaling with reasonable accuracy.

Best,

Oliver

On 19 September 2011 05:44, Yun Shi <yunshi09 at gmail.com> wrote:

> Hi Mark and Justin,
>
> I think I should be more specific here. So i.e., I want to study the
> interaction between a protein receptor and a carbohydrate ligand with MD
> simulation, and I plan to use ff99sb for protein while glycam06 for
> carbohydrate.
>
> Since the two force fields are parameterized using different scaling
> factors, I should use different fudge values, although these values will not
> DIRECTLY affect inter-molecular interactions.
>
> So how to set this up, if it is possible, within .top file and .itp files?
>
> Thanks,
> Yun
>
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