[gmx-users] rvdw and dispersion correction for amber99sb

Yun Shi yunshi09 at gmail.com
Tue Aug 21 07:44:49 CEST 2012

In the original paper [Comparison of multiple Amber force fields and
development of improved protein backbone parameters], 0.8 nm was used;
but I did find recent papers using 1.0 nm for rvdw. And I myself used
1.4 nm, all without obvious abnormality.

On Mon, Aug 20, 2012 at 10:13 PM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> On 21/08/2012 2:30 PM, Yun Shi wrote:
>> Hello all,
>> I am simulating protein-ligand complex with amber99sb force field in
>> TIP3P water. What would be a reasonable value rvdw? I  saw someone
>> uses 1.0, and I did not find any abnormality when using 1.4 nm for
>> rvdw, but where can I find the right reference?
> It's cited in the GROMACS manual. Of course, you read it, and reports of
> similar studies others did with the force field before choosing it,right?
> :-)
>> And is this force field parameterized with or without dispersion
>> correction? (Better to turn it on or off?)
> Generally, one should follow the parametrization strategy, unless/until
> someone shows that observables relevant to yours are unaffected or improved
> by a change.
> Mark
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