[gmx-users] new beta release - gromacs-4.5-beta2
per.larsson at sbc.su.se
Thu Aug 5 22:38:25 CEST 2010
Is this with GBSA implicit solvent, and in that case what Born radii model?
Could you mail me the tpr off-list, and I'll have a look at it.
5 aug 2010 kl. 20.26 skrev Elio Cino:
> 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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