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

[XAvier Periole]

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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