[gmx-users] Force Field for protein in water

[Justin Lemkul]

On 12/17/14 1:16 AM, neha bharti wrote:
> Hello All
>
> I am trying to MD simulation of protein in water and same Protein bound
> with Ligand in water.
> Which force field is good for both the cases.
> I just want to compare the results of bound and unbound Proteins. So,
> Should I use different force fields for both or same force field.
>

You absolutely need to use the same force field.  The one you choose should be 
based on your own scrutiny of literature related to similar systems (What do 
other people use for protein-ligand complexes?  What defects are known in 
protein force fields?) and other practical considerations (Which force field 
allows you to easily create a high-quality topology that you can implement in 
Gromacs?)

-Justin

-- 
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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

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