[gmx-users] Justin tutorial - V-rescale + Parinello-Rahman

[Andrew S. Paluch]

Steven,

I would also suggest reading the following recent publication from the 
Shirt's group:

Simple Quantitative Tests to Validate Sampling from Thermodynamic Ensembles
Michael R. Shirts
J. Chem. Theory Comput., 2013, 9 (2), pp 909–926
DOI: 10.1021/ct300688p

http://pubs.acs.org/doi/abs/10.1021/ct300688p

Andrew

On 04/09/2014 09:50 AM, Steven Neumann wrote:
> Thank you for this!
>
> Steven
>
>
> On Wed, Apr 9, 2014 at 2:14 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> On 4/9/14, 8:18 AM, Steven Neumann wrote:
>>
>>> Dear Gmx Users, Dear Justin
>>>
>>> I have noticed that in in our tutorial(s) in thew mdp option you
>>> suggesting
>>> V-rescale thermostat and the Parinello-Rahman barostat. Is there any
>>> particular reason for this choice? Would you please provide any reference
>>> that is combinantion works well in comparison to others or its just the
>>> example?
>>>
>>>
>> The original references for each of the algorithms prove that they
>> adequately sample the desired ensembles.  For the purposes of tutorials,
>> these algorithms are robust, and I avoid Berendsen because I experience has
>> shown me that people simply assume that whatever is in the tutorial is
>> "correct" so I at least attempt to avoid leading people into making
>> mistakes.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA 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
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
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-- 
Andrew S. Paluch, PhD
Department of Chemical, Paper, and Biomedical Engineering
Miami University
PaluchAS at MiamiOH.edu
(513) 529-0784