i.daidone at caspur.it
Wed Jun 21 14:33:43 CEST 2006
but what about the following gromacs page:
and the following article of van Gunsteren
"J Comp Chem, 1998, 19:535" which suggests the use of 1.4 nm?
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.
> 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.
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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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