[gmx-users] Re: Martini with PME, temp two low
ABEL Stephane 175950
Stephane.ABEL at cea.fr
Thu Apr 25 16:17:00 CEST 2013
@ 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>
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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
>
>
>
> ------------------------------
>
> Message: 5
> Date: Thu, 25 Apr 2013 13:34:21 +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: <4632C83B-CD6F-4C92-B887-A1C39DFF4F94 at rug.nl>
> Content-Type: text/plain; charset=us-ascii
>
>
> Did you visualise the system? T in function of time? Epot in function of time?
>
> As a side note (not relevant for PME) the mix of nstlist = 10 and the rlist = 1.0 is pretty bad! You want at least rlist=1.2 when nstlist=5 and rlist=1.4 if nstlist =10.
>
> On Apr 25, 2013, at 1:10 PM, ABEL Stephane 175950 <Stephane.ABEL at cea.fr> wrote:
>
>> Hello all,
>>
>> I am trying to test the martini force field with PME for a charged system that contains na+, water, surfactant, octane molecules at 298K and P=0.1MPa. My system works well, if i use the standard shift parameters (correct temp, and pressure). But for for the simulation with PME , the temp of the system decrease to 290 K. Below my *.mdp parameters for a NPT equil at 298K
>>
>>
>> integrator = md
>> dt = 0.020
>> nsteps = 10000 ; 200ps
>> nstcomm = 10
>> comm-grps =
>> ;refcoord_scaling = com
>>
>> nstxout = 0
>> nstvout = 0
>> nstfout = 0
>> nstlog = 1000
>> nstenergy = 100
>> ;nstxtcout = 1000
>> xtc_precision = 100
>> ;xtc-grps =
>> energygrps = AOT W ION OCT
>>
>> nstlist = 10
>> ns_type = grid
>> pbc = xyz
>> rlist = 1.
>>
>> ; PME parameters
>> coulombtype = PME
>> rcoulomb = 1.2
>> rvdw = 1.2
>> fourierspacing = 0.12
>> fourier_nx = 0
>> fourier_ny = 0
>> fourier_nz = 0
>> pme_order = 4
>>
>> tcoupl = v-rescale
>> tc-grps = AOT_W_ION OCT
>> tau_t = 1.0 1.0
>> ref_t = 298 298
>> Pcoupl = berendsen
>> Pcoupltype = isotropic
>> tau_p = 1.0
>> compressibility = 4.5e-5
>> ref_p = 1.0
>>
>> ;gen_vel = no
>> ;gen_temp = 0
>> ;gen_seed = 473529
>>
>>
>> ; MARTINI and CONSTRAINTS
>> ; for ring systems and stiff bonds constraints are defined
>> ; which are best handled using Lincs.
>>
>> constraints = none
>> constraint_algorithm = Lincs
>> unconstrained_start = no
>> lincs_order = 4
>> lincs_warnangle = 3
>>
>>
>> Results obtained with W/ PME
>>
>> Statistics over 10001 steps using 1001 frames
>>
>> Energies (kJ/mol)
>> Bond G96Angle LJ (SR) Coulomb (SR) Coul. recip.
>> 1.63789e+04 1.25195e+03 -4.02093e+05 -8.22079e+03 -4.86843e+04
>> Potential Kinetic En. Total Energy Temperature Pressure (bar)
>> -4.41367e+05 7.81801e+04 -3.63187e+05 2.90373e+02 -1.76470e+01
>> T-AOT_W_ION T-OCT
>> 2.90629e+02 2.90357e+02
>>
>> Results W:o PME
>>
>> Energies (kJ/mol)
>> Bond G96Angle LJ (SR) Coulomb (SR) Potential
>> 1.60482e+04 1.24820e+03 -3.34608e+05 -7.33665e+02 -3.18046e+05
>> Kinetic En. Total Energy Temperature Pressure (bar)
>> 8.02685e+04 -2.37777e+05 2.98129e+02 -3.07123e+01
>>
>> Box-X Box-Y Box-Z
>> 1.52926e+01 1.52926e+01 1.52926e+01
>>
>>
>> T-AOT_W_ION T-OCT
>> 2.98141e+02 2.98129e+02
>>
>>
>> Did I miss something ?
>>
>>
>> Note that for the moment i do not use the polarizable water model.
>>
>> Thanks for your help
>>
>> Stephane
>>
>>
>>
>>
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