[gmx-users] Quick question about pressure coupling
jalemkul at vt.edu
Wed Sep 11 15:18:14 CEST 2013
On 9/11/13 9:09 AM, HANNIBAL LECTER wrote:
> 500ps simulations. Yes everything is immersed in a bath of water. Can you
> please elaborate a little more as to why do you doubt semiisotropic
> coupling may not be necessary?
Water should compress isotropically. I understand where you're coming from,
given that you have observed a seemingly semiisotropic compression of the
system, but physically that is not right. Something like a membrane, that has
properties that make it sensible to couple x-y and z compression separately,
would use semiisotropic coupling.
Is this a system in which you're using freezegrps?
> On Wed, Sep 11, 2013 at 9:05 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>> On 9/11/13 9:01 AM, HANNIBAL LECTER wrote:
>>> I am trying to simulate a peptide inside a nanotube and using isotropic
>>> pressure coupling for the system. The nanotube is immersed in a cuboidal
>>> box of water and aligned along the z direction of the box.
>>> The XX, YY components of the stress tensor are about ~570 bars and the ZZ
>>> component is about -1179 yielding a total pressure of about 2 bars whereas
>>> my set pressure is ~1.01325 bars. Is this okay or should I be using
>>> semiisotropic coupling?
>> Over how long a time period are these values? If everything is immersed
>> in a bath of water, I doubt semiisotropic coupling is necessary.
>> Justin A. Lemkul, Ph.D.
>> 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 <jalemkul at outerbanks.umaryland.edu> | (410)
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Justin A. Lemkul, Ph.D.
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
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