[gmx-users] Martini with PME, temp two low
ABEL Stephane 175950
Stephane.ABEL at cea.fr
Thu Apr 25 15:40:48 CEST 2013
Sorry for the double post, but i forgot to remove the others message. I have also added the average values obtained for this run
Statistics over 20001 steps using 4001 frames
Energies (kJ/mol)
Bond G96Angle LJ (SR) Coulomb (SR) Coul. recip.
1.65683e+04 1.26644e+03 -4.02287e+05 -8.47260e+03 -4.90494e+04
Potential Kinetic En. Total Energy Temperature Pressure (bar)
-4.41974e+05 7.91982e+04 -3.62776e+05 2.94154e+02 -1.80237e+01
Box-X Box-Y Box-Z
1.51316e+01 1.51316e+01 1.51316e+01
Total Virial (kJ/mol)
2.90936e+04 -4.68005e+01 -2.46005e+01
-4.68005e+01 2.92687e+04 -2.56235e+01
-2.46006e+01 -2.56236e+01 2.64822e+04
Pressure (bar)
-2.57341e+01 5.58858e-01 1.46893e-01
5.58858e-01 -2.74443e+01 2.21040e-01
1.46893e-01 2.21041e-01 -8.92609e-01
Total Dipole (D)
4.16699e+02 1.92049e+02 6.43137e+02
Epot (kJ/mol) Coul-SR LJ-SR
AOT-AOT 5.26697e+02 -4.94208e+03
AOT-W 0.00000e+00 -2.35002e+03
AOT-ION -9.54002e+03 -1.89339e+03
AOT-OCT 0.00000e+00 -2.04448e+04
W-W 0.00000e+00 -3.88078e+02
Stephane
------------------------------
Message: 4
Date: Thu, 25 Apr 2013 13:26:32 +0000
From: ABEL Stephane 175950 <Stephane.ABEL at cea.fr>
Subject: [gmx-users] RE : gmx-users Digest, Vol 108, Issue 154
To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
Message-ID:
<3E39B768BB199548AB18F7289E7534AF1A818187 at EXDAG0-B0.intra.cea.fr>
Content-Type: text/plain; charset="us-ascii"
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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