Xavier
I have followed your suggestion and did a longer NPT equilibration with smaller
dt and ntlist values and It works. The Energy and Temp reach to stables values
as i want.
thank you again for your help
Stephane
------------------------------
Message: 2
Date: Thu, 25 Apr 2013 14:17:00 +0000
From: ABEL Stephane 175950 <stephane.a...@cea.fr>
Subject: [gmx-users] Re: Martini with PME, temp two low
To: "gmx-users@gromacs.org" <gmx-users@gromacs.org>
Message-ID:
<3e39b768bb199548ab18f7289e7534af1a818...@exdag0-b0.intra.cea.fr>
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@ Vitaly
of course. I know that. My system is neutral but with charged particles (AOT
and Na+).
@Xavier
I will try your suggestion and equilibrate my system for a longer period
Thanks again
Stephane
----------------------------------------------------------------------
Message: 1
Date: Thu, 25 Apr 2013 15:52:09 +0200
From: XAvier Periole <x.peri...@rug.nl>
Subject: Re: [gmx-users] Martini with PME, temp two low
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <0a7b7d0a-b419-4d3d-826b-e6d61de6d...@rug.nl>
Content-Type: text/plain; charset=windows-1252
Well ? 400 ps is rather small and you can expect deviations from so short
simulations if you start from an non-equilibrated system. I am not sure what
the void is but this indicates that your system might not be equilibrated ?
You can try to decrease the time step and nstlist to see if you the drop of
temperature is due a flow of energy.
On Apr 25, 2013, at 3:26 PM, ABEL Stephane 175950 <stephane.a...@cea.fr> wrote:
> Hello Xavier,
>
> Thank you for your response.
>
>>> nstlist = 10 and the rlist = 1.0
> My mistake, i did not changes these values when i switched to PME,
>
> I have rerun the simulations for 400 ps in NPT with these changes and plotted
> Epot and Temp vs Time The Epot and Temp values are not stables. The average
> Temp of the system is better than previously but fluctuate around (294 K)
> instead of 298 K . Note i use gmx4.5.5 to do my calculations.
>
> I have also visualized my system at the end of the NPT run, the na+, water,
> surfactant, octane molecules form a slab with void
>
> What's wrong ?
>
> Stephane
>
>--
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