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

[Dr. Vitaly Chaban]

PME should NOT be used with charged systems, for obvious reasons.


On Thu, Apr 25, 2013 at 4:00 PM, ABEL Stephane 175950
<Stephane.ABEL at cea.fr>wrote:

> 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>
> Message-ID:
>         <CAPXdD+bDiuQWG_3eWZ_0yb=
> AyNLaAF08vt46uSEL4wk_BJgbeg at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
>
> 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
> > >
> > >
> > >
>
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