[gmx-users] High pressure in coarse-grained parametrization

[Mark Abraham]

Hi,

Instantaneous pressure is meaningless. You should get roughly the same
behavior with me integrator.

Mark

On Sat, Apr 7, 2018, 04:13 Alex <alexanderwien2k at gmail.com> wrote:

> Dear all,
>
> Here is a part of the *.mdp file I am using in coarse-grained
> parametrization (Iterative Boltzmann Inversion method) of a molecule by
> votca.
>
> integrator               = sd
> tinit                    = 0
> dt                       = 0.00002
> nsteps                   = 50000000
> init_step                = 0
> ...
> *tcoupl                   = no*
> tc-grps                  = System
> tau_t                    = 0.02
> *ref_t                    = 298.15*
> *Pcoupl                   = no*
> pcoupltype               = isotropic
> tau_p                    = 0.5
> compressibility          = 4.5e-5
> *ref_p                    = 1.0*
> gen_vel                  = yes
> gen_temp                 = 298.15
> gen_seed                 = -1
>
> The temperature is fully fine in each step of IBI, but the pressure is such
> as below in the second step (it is twice in the first step IBI):
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
>
> -------------------------------------------------------------------------------
> Pressure                    1143.92         14    2686.58   -67.2573  (bar)
>
> I was wondering if it is normal as I am using sd integrator? If not, what
> can I do to make it normal?
>
> Thank you.
> Regards,
> Alex
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