[gmx-users] protein complex
jalemkul at vt.edu
Tue Oct 20 00:44:32 CEST 2015
On 10/19/15 9:56 AM, Sana Saeed wrote:
> thanks for your reply. but i want to simulate it in gas phase. and i don't know
> which steps to follow.
Vacuum protein simulations have been discussed recently; check the archives and
try Google. The protocol is simple. Energy minimizaation, then a non-PBC
simulation with zero cutoffs. Whether or not there is an additive force field
that can adequately model the gas phase is another story. Additive biomolecular
force fields overestimate gas-phase dipoles to mimic condensed-phase behavior.
> On Monday, October 19, 2015 4:30 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> On 10/19/15 1:21 AM, Sana Saeed wrote:
> > i am working on complex of a protein , it has 5 chain and i want to simulate
> the whole complex at the same time. can anyone help me in the procedure please.
> It's no different than simulating a single protein.
> 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 <mailto:jalemkul at outerbanks.umaryland.edu> |
> (410) 706-7441
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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