[gmx-users] pressure scaling and hard drive space

[David van der Spoel]

Brian Stephenson wrote:
> 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).

It really shouldn't be that hard, so I suspect that there might be other 
problems than just the systems. A good way of testing is to simplify the 
setup. First small systems with cutoff, then large systems with cutoff 
then with PME. Also you start without pressure scaling, i.e. relax first 
at NVT and when energies stabilize add pressure scaling. Same with pos res.

1. NVT with posres on protein and cut-off
2. NVT with posres on protein and PME
3. NPT with posres on protein and PME
4. NPT without posres and with PME

As you probably know the ffgmx2 field is not recommended, we usually 
suggest GROMOS96 for united atom and OPLS/AA for all-atom simulations.


> 
> 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
>  >
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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