[gmx-users] force fields selection
baptista at itqb.unl.pt
Wed Sep 23 17:40:19 CEST 2015
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:
> 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
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