[gmx-users] Re: Simulating a semi-membrane protein

Justin Lemkul jalemkul at vt.edu
Tue Jul 23 15:11:03 CEST 2013

On 7/23/13 7:46 AM, pavithrakb wrote:
> Sir,
> I'm new to simulation. is there any papers or materials (book or website) to
> learn about the forcefields and their limitations. All the advice I get from
> people is to select a ff and membrane based on the previous works on that
> protein or protein family. I know its too much to ask but, can you please
> suggest some papers/materials on forcefields and selecting a membrane. I'm
> sure it will be useful to many beginners like me.

You already have a good starting point - identify what others do.  Precedent is 
important.  Then ask yourself, why are others doing what they are doing?  To 
answer that question requires quite a bit of reading.  Several days spent 
reading about different force fields will save you months of wasted time if you 
blindly choose a poor one for your simulations.  The primary literature for many 
force fields goes back over the course of decades, which will give you an 
appreciation for the underlying design, assumptions, and implementation of a 
force field.  More recent articles certainly exist that have challenged these 
force fields under different conditions.

Websites and textbooks would be convenient, but I have never seen anything 
comprehensive on this topic.  Maybe someone else has and can suggest it.  There 
is, however, a vast amount of literature that tests different force fields. 
Some names that come to mind include Bert de Groot and Robert Best, who I know 
have published several very nice force field comparisons, in addition to the 
publications of the labs from which the force fields originate.  Expect to 
occupy a lot of time reading before doing any simulations - it is time well spent.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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