Good. Note however that we do get the right temperature with a dt=20fs with
Martini so you energy leak might be in the cutoff scheme or the system is
really badly equilibrated.
On Apr 25, 2013, at 18:23, ABEL Stephane 175950 wrote:
> 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 +
> From: ABEL Stephane 175950
> Subject: [gmx-users] Re: Martini with PME, temp two low
> To: "gmx-users@gromacs.org"
> Message-ID:
><3e39b768bb199548ab18f7289e7534af1a818...@exdag0-b0.intra.cea.fr>
> Content-Type: text/plain; charset="us-ascii"
>
> @ 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
> Subject: Re: [gmx-users] Martini with PME, temp two low
> To: Discussion list for GROMACS users
> 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
> 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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