[gmx-users] RE: Martini with PME, temp two low

[XAvier Periole]

nstlist of 2 is a be extreme! Did you try 5! It should be fine … but if your are happy that's ok :))

On Apr 26, 2013, at 12:37 PM, ABEL Stephane 175950 <Stephane.ABEL at cea.fr> wrote:

> Hi Xavier, 
> 
> I used a dt of 10 ps with nstlist of 2. In that case the Temp of the system is stable and the energy well conserved (400 ns of run). I do know if it is optimal but it works for my system. 
> 
> Stephane
> 
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Fri, 26 Apr 2013 07:58:12 +0200
> From: XAvier Periole <x.periole at rug.nl>
> Subject: Re: [gmx-users] Re: Martini with PME,  temp two low (ABEL
>        Stephane 175950)
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
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> 
> 
> 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 <Stephane.ABEL at cea.fr> 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 +0000
>> From: ABEL Stephane 175950 <Stephane.ABEL at cea.fr>
>> Subject: [gmx-users] Re: Martini with PME, temp two low
>> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
>> Message-ID:
>>       <3E39B768BB199548AB18F7289E7534AF1A8181D4 at 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 <x.periole at rug.nl>
>> Subject: Re: [gmx-users] Martini with PME, temp two low
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Message-ID: <0A7B7D0A-B419-4D3D-826B-E6D61DE6D143 at 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.ABEL at 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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