[gmx-users] still about the opls methanol box

ioannis.nicolis at free.fr ioannis.nicolis at free.fr
Fri Oct 4 10:50:35 CEST 2002

Thanks for your suggestions. So here are the news.

First of all I checked my cut-offs. I have :

rlist                    = 1.0
coulombtype              = pme
rcoulomb-switch          = 0
rcoulomb                 = 1.0
vdw-type                 = Cut-off
rvdw-switch              = 0
rvdw                     = 1.4

which seems quite strqnge, I thought I had rcoulomb to 1.4 but maybe it's 
irrelevant for PME?

Anyway the box size is about 4.8 so it's not a problem of having a cut-off 
less than half the box edge.

The machine is a G4 macintosh under OS X version 10.1 and mdrun 
uses altivec loops.

I tried then to test if the crash is reproducible. The previous run crashed at 
221ps and I recorded at the trr every 100ps, so I began from 200ps giving 
the -t option in grompp. The run is now at 61ps, so it passed the previous 
crash point by 40ps and continues OK. But it is not exactly 
superimposable to the corresponding portion of the previous run. I think 
this is normal when you continue a run?
I attach a small png graph of the densities, in black points the first run 
(crashed at 221ps) and in red line the second, continued from 200ps.

Your comments? Thanks again,

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