[gmx-users] NPT MD and Berendsen

[Michael Shirts]

A nonisotropic system will not necessarily end up with exactly the applied
pressure -- things like surface tension and stresses/strains end up getting
mixed in and throwing things off.


On Mon, Jun 23, 2014 at 3:32 PM, Chetan Mahajan <chetanvm10 at gmail.com>
wrote:

> Thanks.
>
> Average was taken over 1000 ps. Error estimate is 2.9 which is smaller than
> average pressure of 19.87 bar. Here is the complete statistics:
>
> Energy                      Average     Err.Est.      RMSD  Tot-Drift
>
> -------------------------------------------------------------------------------
> Temperature              299.968      0.013    1.98625   0.062225  (K)
> Pressure                    19.8699        2.9       726.924    13.5906
>  (bar)
>
> Interestingly, average pressure is close to one (0.86 or 0.8 bar) when
> refcoord scaling of -all is used for position restraints. Above simulation
> where average pressure is so large was carried out with refcoord-scaling of
> -com option. I am simulating TiO2 crystal solvated by water, formate and
> sodium ion. Now, one important observation is that with -com option,
> crystal slab moves a distance during change of box dimensions in NPT
> equilibration, whereas slab DOES NOT move with -all option. However, -com
> option is more favorable since very less water manage to get on the side
> surfaces of slab compared to that in -all option, where lot of water get on
> the side which is not desirable.
>
> What is happening here? Is it because of slab movement that average
> pressure is annoyingly large in simulations with -com option? what can be
> done to rectify or is it okay to proceed anyways?
>
> Thanks a lot!
> regards
> Chetan
>
>
>
> On Mon, Jun 23, 2014 at 1:47 AM, Francis Jing <francijing at gmail.com>
> wrote:
>
> > How long was the average taken over? If the error is larger than the
> > pressure itself, you cannot make judgment.
> > Generally Berendsen is only inaccurate about the fluctuations, not the
> mean
> > value.
> >
> >
> > Francis
> >
> >
> > On Mon, Jun 23, 2014 at 1:50 PM, Chetan Mahajan <chetanvm10 at gmail.com>
> > wrote:
> >
> > > Dear All,
> > >
> > > I am using Berendsen barostat and thermostat for NPT equilibration MD
> run
> > > at 1 atm and 300 K. While it runs fine, average pressure at the end of
> > the
> > > run is 19 bar. I am confused whether this is way off 1 atm target, or
> is
> > > justified recalling gromacs manual that says Berendsen barostat does
> not
> > > yield correct thermodynamic ensemble.
> > >
> > > IN addition, initial box elongates to have space at both ends in
> > > z-direction as can be seen in following link:
> > >
> > > https://www.dropbox.com/sh/dahnyy3zy6vb1xh/AAD5ppxrm18rB3DHZ0Qji0qva
> > >
> > > Again, I am not sure if this is a case for concern or just artifact of
> > > using Berendsen.
> > >
> > > Is Parrinello-Rahman better than Berendsen, even for initial NPT
> > > equilibration?
> > >
> > > Thanks
> > > Chetan
> > > --
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> >
> > --
> > Zhifeng (Francis) Jing
> > Graduate Student in Physical Chemistry
> > School of Chemistry and Chemical Engineering
> > Shanghai Jiao Tong University
> > http://sun.sjtu.edu.cn
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