[gmx-users] force fields selection

[Antonio Baptista]

On Tue, 22 Sep 2015, Justin Lemkul wrote:

>
>
> On 9/21/15 10:22 PM, James Lord wrote:
>> Dear gmx users,
>> 
>> I want to use either gromos 43a2 or 54a7 in Gromacs to simulate protein
>> partitioning at biphasic liquid-liquid interfaces (Similar Justin's
>> tutorial for biphasic system). Which one is recommended if anyone has
>> experience with such system and why? appreciate any comments? I know 54a7
>> is newer version but does it mean it is the best I mean in terms of
>> reproducing experimental data etc? or is there any well known problems with
>> 43a2 for such a system?
>> 
>
> 54a7 corrected a well-known problem in 53a6 with helices being unstable. 
> Previous version (45a3, 43a1, etc) did not have that problem.

If you are concerned with helix stability and/or dynamics, 54a7 is 
probably a good choice. For example, it reproduces the thermodynamics and 
kinetics of a model peptide used in helix nucleation studies: 
http://dx.doi.org/10.1021/ct400529k

>
> -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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