On 9/11/13 9:20 AM, HANNIBAL LECTER wrote:
Yes
Then I would call your outcome an artifact of a physically unreasonable setup.
-Justin
On Wed, Sep 11, 2013 at 9:18 AM, Justin Lemkul <jalem...@vt.edu> wrote:
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?
-Justin
On Wed, Sep 11, 2013 at 9:05 AM, Justin Lemkul <jalem...@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
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Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
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Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
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jalem...@outerbanks.umaryland.edu | (410) 706-7441
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