[gmx-users] a suitable forcefield for ions
jalemkul at vt.edu
Wed May 25 13:35:38 CEST 2016
On 5/25/16 7:31 AM, mah maz wrote:
> Thanks Erik. I found nonbonded parameters for atoms only in Amber ff. Can I
> use them for ions or they are already for ions?
> eg. for Na sigma= 0.332 and epsilon=0.0115. Does it mean that we can use
> thIS sigma and epsilon for Na+?
You should spend some time in the literature; there is a long history of ion
parametrization and refinement, with subsequent discussion of which parameters
are best for what application. This is not an issue that is solved simply by
perusing GROMACS force field files.
All of the force fields in GROMACS have ion parameters; it's up to you to decide
which, if any, of these is suitable for whatever type of simulation(s) you want
> On Wed, May 25, 2016 at 2:11 PM, mah maz <mahmaz71 at gmail.com> wrote:
>> Hi all,
>> i need forcefield parameters for ions. can anyone tell me which forcefield
>> contains ions? can i do ion simulations with amber ff?
>> Thank you
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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