[gmx-users] Exploding/Expanding Box on Different Versions
spoel at xray.bmc.uu.se
Fri Jan 23 17:12:00 CET 2004
On Fri, 2004-01-23 at 02:08, Dallas Warren wrote:
> Finally got some time to get back to this problem ....
> Problem/issue is that from the same trr, gro, mdp and forcefield files,
> with two different versions of GROMACS the molecular system behaves
> differently (one is stable, other explodes).
> Recent (1-2 days ago) CVS version (3.2.0) things are stable. This in on my
> local Linux workstation.
> Last full release version (3.1.4) things are not. This is on the APAC
> Linux cluster.
> Looking at the energies for both simulations:
> Proper Dihedral
> Improper Dihedral
> Coulomb LR
> LJ (SR) - same to start with, within 10ps 3.1.4 version is
> 30,000 higher, -60,000 versus -90,000
> Disper. Corr. - starts 250,000 different, 3.1.4 at ~270,000
> Coulomb SR - starts the same then within 10ps 3.1.4 is
> 35,000 higher
> Taking the tpr file from 3.1.4 and running it on the CVS I get the same
> behaviour as if the tpr file was generated with the CVS version. All the
> energies follow similar values, box volume is stable etc.
> What is going on here?
You didn't say, but are you using a twin range cut-off for Van der Waals
interactions? There a bug was found not so long ago that has been fixed
in the latest version. To be more precise one octant of the Long range
bit was not taken into account. Energy differences are small. Another
error could lie in the dispersion correction: is your system more than
> With the same md.mdp parameters and very similar molecular systems (same
> molecules, water, mono- and di-glycerides, just slightly different amounts)
> I had previously been running things on 3.1.4 without an issue! And other
> systems are currently running fine!
> Catch ya,
> Dr. Dallas Warren
> Research Fellow
> Department of Pharmaceutical Biology and Pharmacology
> Victorian College of Pharmacy, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.warren at vcp.monash.edu.au
> +61 3 9903 9083
> When the only tool you own is a hammer, every problem begins to resemble a nail.
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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
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