[gmx-users] new beta release - gromacs-4.5-beta2

Szilárd Páll szilard.pall at cbr.su.se
Thu Aug 5 21:24:19 CEST 2010


Could you provide the compiler versions you used? I really hope it's
not gcc 4.1.x again...


On Thu, Aug 5, 2010 at 8:26 PM, Elio Cino <ecino at uwo.ca> wrote:
> Since the charmm force field has some instances with large charge groups
> (grompp warns you for it) it is advisable to use a longer cut-off (or no
> cut-off at all, by setting them all to 0). I've run 200 ns simulations  with
> 1.5 nm and nstlist = 5 and a timestep of 2 fs and constraints =  all-bonds.
> I could not have them set to infinite because I am using PBC. I used 1.5 and
> the system ran fine with 2fs timestep. On another note, I installed 4.5
> beta2 on another computer today and using the exact same system and settings
> I get tons of lincs errors (bond rotate over 30 deg) and cannot even do
> position restrain dynamics without segmentation fault. I even tried using
> the exact same tpr files as my successful runs.  The one that works was my
> laptop (OSX 10.6 core2 duo) and the one that fails is centos5 dual quad core
> xenon. If I run a normal solvated simulation, the linux machine runs fine.
> Elio Cino
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