[gmx-users] Semiisotropic Pressure coupling with PR

Sai Pooja saipooja at gmail.com
Thu Jul 15 16:13:43 CEST 2010

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?


On Thu, Jul 15, 2010 at 10:02 AM, Justin A. Lemkul <jalemkul at vt.edu> 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
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> ========================================
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> 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.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100715/5ccda01e/attachment.html>

More information about the gromacs.org_gmx-users mailing list