[gmx-users] the relationship between mdp file and the force field

[Justin Lemkul]

On 4/27/15 9:01 AM, Brett wrote:
> Dear Justin,
>
>
> I have read some of the force fields original paper, but my purpose is to use
> MD to settle some biological issues, thus I am afraid I do not have such deep
> understanding what explained in the original force field papers.
>
> For Force field 6, here I mean AMBER99SB_ILDNprotein. For the MDP files, I
> think  AMBER99SB_ILDNprotein force field, AMBER99SB protein, AMBER 99
> protein, AMBER 96 protein can have the same mdp files, GROMOS96 43a1, 43a2,

I don't think that's true.  I know the AMBER99sb-ILDN paper gives the 
appropriate details for how to treat nonbonded interactions.

> 45a3, 53a3, 53a5,53a6,54a7 can have the same MDP files, am I right? If we

GROMOS usage doesn't change, so that's correct.

> modified based on the on-line lysozyme tutorial, what items should we modify
> based on the original lysozyme mdp diles?
>

Anything related to nonbonded interactions - rlist, rcoulomb, rvdw, vdwtype. 
PME is generally used nowadays for everything, so that's common.

> In addition, for biological research, can we definetely say GROMOS96 54a7 is
> better than the other versions of GROMOS96? In comparision with the GROMOS
> series, what is the advantages and disavantages of OPLS-AA/L all-atom force
> field?
>

"For biological research" is way too broad.  Some force fields fare better than 
others for disordered proteins vs. folded proteins.  "Biological" also 
encompasses membranes, nucleic acids, etc. and these force fields all vary 
wildly in their abilities to model those systems.

You need to identify similar systems and see how well different force fields 
have fared.  Define your problem narrowly.

-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 | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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