[gmx-users] Barostat & Density decreasing to zero

[Ran Friedman]

Hi Omer,
You use a  dielectric constant is 80, which means that the electrostatic
interactions are screened. Perhaps that's why your density is low.
Ran.

Omer Markovitch wrote:
> Dear All,
> I have simulated a protein inside a box with water and ions. I began
> by minimizing my system (which has a total charge of zero), until the
> maximum gradient was small enough and the potential energy become
> negative.
> Then I heated it, slowly, to 300K at constant volume (using berendsen
> thermostat and tcoupl = 1 ps).
> Then I performed 500 ps NVT simulation to equilibrate the temperature,
> at 300K.
> Then, I tried to equilibrate the pressure and run NPT simulation,
> using Berendsen barostat (p=1, pcoupl=10) and Berendsen thermostat
> (T=300K, tcoupl = 0.1).
>
> My problem is, that with the barostat & thermostat both active in the
> same MD run, my density drops to a very low value (at the first MD
> steps, the density is 1000, dropping later to 100 kg/m^3). That is- my
> box dimensions increase significantly (from around 6x6x6 to 12x12x12
> nm^3. If I change the pressure coupling constant, the speed of the
> expansion changes but all simulation converged to a small density
> between 50-100 kg/m3.
>
> Your help is appreciated; Probably, I am not controlling the
> simulation like I should. I will appreciate any advice.
> Thank you, Omer Markovitch.
>
> I have used gromacs version 3.3.3, Here is my .MDP file for the NPT run:
>
> integrator               = md
> dt                       = 0.001
> nsteps                   = 500000
> comm_grps                = system
> nstxout                  = 500
> nstvout                  = 500
> nstcheckpoint            = 1000
> nstlog                   = 500
> nstenergy                = 500
> nstlist                  = 10
> ns_type                  = simple
> pbc                      = xyz
> rlist                    = 1.0
> coulombtype              = PME
> rcoulomb-switch          = 0
> rcoulomb                 = 1.0
> epsilon_r                = 80
> epsilon_rf               = 80
> vdw-type                 = Cut-off
> rvdw-switch              = 0
> rvdw                     = 1.0
> table-extension          = 1
> fourierspacing           = 0.12
> pme_order                = 4
> ewald_rtol               = 1e-05
> ewald_geometry           = 3d
> optimize_fft             = yes
> tcoupl                   = berendsen
> tc-grps                  = system
> tau_t                    = 0.1
> ref_t                    = 300
> Pcoupl                   = berendsen
> Pcoupltype               = Isotropic
> tau-p                    = 10
> compressibility          = 4.5E-5
> ref-p                    = 1
> andersen_seed            = 815131
> constraints              = none
>
> ------------------------------------------------------------------------
>
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