[gmx-users] force fields selection

[James Lord]

Hi Antonio,

Thanks for further information and the paper.

Cheers
James

On Thu, Sep 24, 2015 at 3:30 AM, Antonio Baptista <baptista at itqb.unl.pt>
wrote:

> 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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