Re: system becomes very large when set LangevinPiston on

From: nordgren_at_sas.upenn.edu
Date: Tue Jul 26 2005 - 12:20:50 CDT

The NAMD units of pressure are indeed in bars.

However, in a typical constant-pressure simulation, the short-term average
pressure of the system (PRESSAVG) will typically fluctuate by hundreds of
bars, and the instantaneous value (PRESSURE) will often be in the thousands.

Moreover, you *may* see PRESSURE values that can look quite large (say, in
the tens of thousands) -- if you are using multiple-timestepping, but
printing energies every step. This is because the long-range forces are not
being computed every step, and so when you look at the instantaneous pressure
during those off-steps, the numbers look pretty wild. (But it all comes out
correctly in the end.)

IMO, the only parameter really worth paying much attention to is "PRESSAVG"
(or better, "GPRESSAVG"), and even then it is most meaningful when you look
at its longer-term average trend (which *should* be close to your specified
value of 1 atm or whatever).

hope this helps...

C. Erik Nordgren, Ph.D.
Department of Chemistry
University of Pennsylvania

Quoting Xiaoqing Wang <namdwxq_at_126.com>:

> Hi,
>
> What's the unit of the item PRESSURE of output file?
> In the equil.namd input script file the LangevinPistonTarget is set to
> 1.01325(bar). In my output file the PRESSURE is about 0 in the end. But
> in the output(equil.log) file which I downloaded from
> http://www.ks.uiuc.edu/Research/namd/tutorial/NCSA2002/hands-on/sample/
> the PRESSURE value is about 1000 in the end.
>
> Sincerely,
> Xiaoqing
>
>
> 在2005年07月25日的11:06,Xiaoqing Wang写道:
> > Dear all,
> >
> > I downloaded "fftw-linux-amd64.tar.gz" and "tcl-linux-amd64.tar.gz" from
> > http://www.ks.uiuc.edu/Research/namd/libraries/ and plugins for
> > LINUXAMD64 and "charm-net-linux-amd64.tar.gz" from
> > http://charm.cs.uiuc.edu/autobuild/bin/ and NAMD_2.5_Source.tar.gz.
> >
> > I compiled NAMD with
> > ./config tcl fftw plugins Linux-amd64-g++
> > ./make
> >
> > I download input files from web site :
> > http://www.ks.uiuc.edu/Research/namd/tutorial/NCSA2002/hands-on/sample/
> > and run "namd2 equil.namd>equil.log" on AMD64 opteron.
> >
> > When run equilibrate with langevinPiston on
> > ---------------------------------------------
> > # equilibrate volume with CAs restrained
> > langevinPiston on
> > run 5000
> > output equil_ca
> > ---------------------------------------------
> > the systerm becomes very large and disperse.
> >
> > I compiled many times and run many other examples and found that all of
> > the systerms become disperse when set "langevinpiston on". I don't know
> > why the pressure value is incorrect and the pressure control can't work.
> >
> >
> > Any tips would be greatly appreciated!
> >
> --Xiaoqing
> Wuhan University
> Wuhan 430072
> China

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