[gmx-users] NPT MD and Berendsen

[Chetan Mahajan]

Thank  you, Dr. Shirts. My pressure coupling type is also semi-isotropic.
So is that simulation worth at all  ( since equilibration not on intended
pressure even remotely) or we need to discard the simulation totally ?

Also, this high pressure (and crystal slab movement ) occurs only with
refcoord-scaling option of -com and not with -all. I wonder why.

Thanks.

regards
Chetan

On Mon, Jun 23, 2014 at 3:35 PM, Michael Shirts <mrshirts at gmail.com> wrote:

> 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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