[gmx-users] protein complex

[Justin Lemkul]

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.

-Justin

>
>
> On Monday, October 19, 2015 4:30 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
>
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> 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
>
> --
> ==================================================
>
> 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
> http://mackerell.umaryland.edu/~jalemkul
>
>
> ==================================================
>
>

-- 
==================================================

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
http://mackerell.umaryland.edu/~jalemkul

==================================================