[gmx-users] NVE problems
David van der Spoel
spoel at xray.bmc.uu.se
Sat Dec 27 21:11:01 CET 2003
On Sat, 27 Dec 2003 istvan at kolossvary.hu wrote:
>I posted a message right before Christmas (gmx-users digest, Vol 1 #1166)
>about problems with NVE. I have a feeling that the nsgrid error that I
>mentioned is not specific to the problem, it just shows a general numerical
>instability due to the NVE simulation. In other cases Gromacs blows up with
>other numerical errors. In any case, I guess the simplest way to present the
>problem is to ask why should Gromacs blow up on alanine dipeptide in a 3x3x3
>nm box using NVE instead of NPT? I can hardly think of anything simpler. The
>system was minimized, PR-equilibrated (FF was OPLS-AA), but then a fully
>unconstrained run with PME that would normally run without problems in NPT,
>blows up after only 1 ns using a 1 fs time step when I turn off temperature
>and pressure control. Shouldn't a 1 fs time step be adequate for NVE without
>LINCS/SHAKE? Can anyone experienced with NVE in Gromacs help me?
I think it is too long a time step. 0.5 fs is probably the maximum for
stability with T coupling, but you may even need shorter without. Check
for energy components. Are bond/angle energies getting out of hand? What
water do you use? Is it with settle?
> Istvan Kolossvary
>gmx-users mailing list
>gmx-users at gromacs.org
>Please don't post (un)subscribe requests to the list. Use the
>www interface or send it to gmx-users-request at gromacs.org.
David van der Spoel, PhD, Assist. 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://xray.bmc.uu.se/~spoel
More information about the gromacs.org_gmx-users