Sai Pooja wrote:
1. Pressure
For my initial configuration, I run a long nvt run. This gives me a
pressure. Then I run an npt simulation at this prerssure.
The idea is to do expansion runs(decrease pressure so that the system
expands) to get a P vs density curve.
For example, after I determine the pressure of the initial configuration
from the long nvt run, say Pinit, I choose a set of pressures - Pinit,
P1, P2...., PN s.t Pinit>P1,>P2...(eg. 74, 72, 70, 69.....50). Then for
each pressure I run an npt simulation till the average converges.
2. Freeze-dimension
Is there a better alternative for running simulations for a planar system?
Maybe you want to use "pbc = xy" or walls? Is there any literature precedent
for what you want to do, or perhaps an alternate procedure?
-Justin
Pooja
On Thu, Jul 15, 2010 at 10:02 AM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
Sai Pooja wrote:
<snip>
Do you run any equilibration prior to applying these parameters?
Both N-H and P-R allow for wide fluctuations in temperature and
pressure, respectively, which are exacerbated by systems that are
not sufficiently equilibrated. Hence it could take a very
long time
if you do not equilibrate well using, i.e. a weak coupling
scheme first.
I usually start with a pressure nearby. For example, I start
with a system which was equilibrated at p=71 and then run npt at
p=69. Is that not sufficient?
How do you determine the pressure before the simulation has begun?
Moreover, freezing your system in one dimension can certainly
complicate matters, since that is a non-equilibrium restraint on the
dynamics. That could be a factor.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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