[gmx-users] rvdw

[Tsjerk Wassenaar]

Oops..., indeed, Gromos was parameterized for use with 1.4 nm :S
Should also have checked my sources first. Scuziscuziscuzi...

Tsjerk

On 6/21/06, Isabella Daidone <i.daidone at caspur.it> wrote:
>
> Thanks Tsjerk,
>
> but what about the following gromacs page:
> http://www.gromacs.org/blogcategory/page_4.html
> and the following article of van Gunsteren
> "J Comp Chem, 1998, 19:535" which suggests the use of 1.4 nm?
>
> Thanks
> Isabella
>
> On Wed, 21 Jun 2006, Tsjerk Wassenaar wrote:
>
> > Hi Isabella,
> >
> > The Gromos force fields were parameterized for use with a rvdw cutoff of
> 0.9.
> > Other cutoffs may introduce artefacts.
> >
> > Ciao!
> >
> > Tsjerk
> >
> > On 6/21/06, Isabella Daidone <i.daidone at caspur.it> wrote:
> >>
> >> Sorry, but I'm a little bit confused about what rvdw to use for
> >> simulations of proteins in solution with gromos96 force field while
> using
> >> pme for
> >> coulomb interactions.
> >> In the gromacs 3.3 manual I still read (with pme):
> >> rcoulomb=rlist=rvdw=0.9 nm
> >>
> >> Then, I found in the discussion list (+ the paper J Comp Chem,
> >> 1998, 19:535) someone suggesting rvdw=1.4 nm.
> >>
> >> Could you please help me? what's your suggestion?
> >> Is it nowadays anyway accepted to
> >> use rcoulomb=rlist=rvdw=0.9 nm?
> >> And is there any difference between the standard G43a1 version or the
> >> newest (G53a...)?
> >>
> >> Thank you very much.
> >>
> >> Isabella
> >>
> >>
> >>
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> >
> >
> >
> > --
> >
> > Tsjerk A. Wassenaar, M.Sc.
> > Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
> > Dept. of Biophysical Chemistry
> > University of Groningen
> > Nijenborgh 4
> > 9747AG Groningen, The Netherlands
> > +31 50 363 4336
> >
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-- 

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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