[gmx-users] Semiisotropic Pressure coupling with PR
saipooja at gmail.com
Thu Jul 15 16:28:47 CEST 2010
Its basically a melting process and there is ample of published data on this
(not related to gromacs though). The only reason for using freeze-dimensions
was to avoid using pbc=xy in combination with walls since I thought the
extra interactions due to the walls might make the simulations
The data I have obtained from these runs doesn't seem to match with an npt
MC simulation(fortran based in-house code) and the data from the MC
simulation looks more credible when compared to published results.
On Thu, Jul 15, 2010 at 10:21 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> 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?
>> On Thu, Jul 15, 2010 at 10:02 AM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>> jalemkul at vt.edu>> wrote:
>> Sai Pooja wrote:
>> 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
>> 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 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
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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
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Quaerendo Invenietis-Seek and you shall discover.
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