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.abra...@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 > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Only plain text messages are allowed! > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
