[gmx-users] Exploding/Expanding Box on Different Versions

Dallas Warren dallas.warren at vcp.monash.edu.au
Fri Jan 23 03:03:01 CET 2004

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?

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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