[gmx-users] a suitable forcefield for ions
jalemkul at vt.edu
Wed May 25 13:43:06 CEST 2016
On 5/25/16 7:40 AM, mah maz wrote:
> Thanks Justin. I can only find atoms in ffnonbonded.itp in Amber ff. Where
> should I search for ions parameters in Amber ff?
Every force field has an ions.itp file. Look for those atom types. But knowing
those values won't really tell you anything on their own. You need to know (1)
the literature source of those parameters and (2) the pros/cons to those
parameters, also in the literature.
> On Wed, May 25, 2016 at 4:01 PM, mah maz <mahmaz71 at gmail.com> 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+?
>> 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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