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

[ABEL Stephane 175950]

And ? sorry but i do not understand...

Stephane

------------------------------

Message: 2
Date: Thu, 25 Apr 2013 15:39:12 +0200
From: "Dr. Vitaly Chaban" <vvchaban at gmail.com>
Subject: Re: [gmx-users] Martini with PME, temp two low
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
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Hmmm....

Aren't the keywords here "charged system" + "PME"?


Dr. Vitaly Chaban



On Thu, Apr 25, 2013 at 1:34 PM, XAvier Periole <x.periole at rug.nl> wrote:

>
> 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
> >
> >
> >