[gmx-users] pressure scaling and hard drive space

[Brian Stephenson]

I have played around with tau_p, even increasing it to very high values 
such as 100
and still get the pressure scaling problems.  I've also energy minimized 
many times,
to no avail.  For this particular system I've been thinking there isn't 
anything very
unphysical going on ... for some of the smaller systems I've simulated 
after managing
to get the system to simulate for 100 ps or so it becomes much more 
stable.  I think
I simply need to get some equilibration behind me for these larger systems 
as well.
If I simulate under NVT conditions I get seg faults at first but again 
after getting some
simulation time behind it I believe the system could become stable.  The 
problem is
getting there.  Simulations of the dendrimer in vacuum are stable, so it 
shouldn't
be a problem in the definition of the dendrimer topology.

Btw, I've tried various tau_t and tau_p values, simulating with and without 
bond constraints,
changing the simulation temperature, changing the ratio of solute (a 
dendrimer) to solvent,
changing the simulation geometry (cubic box vs. dodecahedron), decreasing 
the timestep,
etc.  Actually the only thing that has (kind of) worked has been running 
with a different
(older) version of GROMACS, which seems a bit more stable during initial 
equilibration.
I'm using PME electrostatics, but the system is nonionic so that shouldn't 
matter too much.
The FF is ffgmx2, and the water model is SPCE or SPC (both give the same 
problems).

But these pressure scaling problems keep maxing out my harddrive, when I would
rather that the simulation would just crash or at least not continually 
write the
error message to file.  Any ideas on either getting around this period of 
instability
or turning off the pressure scaling errors?

Thanks,
-Brian



Message: 4
Date: Sat, 25 Feb 2006 09:48:00 +0100
From: David van der Spoel <spoel at xray.bmc.uu.se>
Subject: Re: [gmx-users] pressure scaling and hard drive space
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID: <440019C0.4020002 at xray.bmc.uu.se>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

Brian Stephenson wrote:
 > Anyone know how to turn off those pesky "pressure scaling is greater
 > than 1%" error messages?  Instead of crashing, my simulations keep
 > running with errors and I keep running out of hard drive space when the
 > simulation keeps sending out the warnings over and over again.   I'm
 > using mdrun with the -v flag, and maybe not using the -v would get rid
 > of them (?) but I need to know how much time is left for my jobs.

if you get these warnings often your simulation is really behaving
unphysically because something is wrong.
Are you sure your simulations are OK?

If you scale temperature or pressure too fast the whole system can
become unstable.
 >
 > Thanks,
 > Brian



Message: 1
Date: Sat, 25 Feb 2006 08:34:05 -0300
From: paloureiro at biof.ufrj.br
Subject: Re: [gmx-users] pressure scaling and hard drive space
To: gmx-users at gromacs.org
Message-ID: <20060225083405.eaw5hznpranko8wc at webmail.biof.ufrj.br>
Content-Type: text/plain;	charset=ISO-8859-1;	format="flowed"

Hi Brian,

if you are using Berendsen pressure coupling (and your system is in the
equilibration phase) try increasing tau-p.

Regards.

Pedro.


 > Anyone know how to turn off those pesky "pressure scaling is greater
 > than 1%" error messages?  Instead of crashing, my simulations keep
 > running with errors and I keep running out of hard drive space when
 > the simulation keeps sending out the warnings over and over again.
 > I'm using mdrun with the -v flag, and maybe not using the -v would
 > get rid of them (?) but I need to know how much time is left for my
 > jobs.
 >
 > Thanks,
 > Brian
 >