[gmx-users] Semiisotropic Pressure coupling with PR

[Sai Pooja]

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
computationally intensive.

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.

Pooja

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?
>
> -Justin
>
>
>> Pooja
>>
>>
>> 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:
>>
>>    <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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>>
>> --
>> Quaerendo Invenietis-Seek and you shall discover.
>>
>
> --
> ========================================
>
> 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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-- 
Quaerendo Invenietis-Seek and you shall discover.
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