[gmx-users] NPT MD and Berendsen

[Chetan Mahajan]

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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