[gmx-users] Re: Diatomic in MeCN NPT (NH and PR) simulation segfaults after 1 us

benjfitz benjfitz at gmail.com
Tue Nov 6 05:25:48 CET 2012

Justin, thank you for reminding me that I need to adhere to sane parameters.
I do have a few clarifying points, as it were. I tried these simulations
again, but with a larger box and 0.9 nm cutoffs, and received a segfault at
the same simulation time.

The model I am using, from the user contributed downloads section, does make
use of virtual sites (virtual2). The choice for the masses and diatomic bond
length always seemed strange to me (9 and 33 amu) b/c one could use almost
identical masses. This would make setting up the virtual sites far more
intuitive. I did this, after going through your tutorial for CO2, and this
adaptation of the MeCN model suffers the same instability. 

I then took your CO2 model and modified it to CS2 using the proper LJ
parameters from Madden's 1981 model that doesn't have charges. I ran this
using coulombtype=cutoff and the 2 us simulation completed without any
problems. I gave small (-0.01 for S and 0.02 for C) charges to the atoms and
ran using PME, which crashed at 1.07 us.

Do these results shed any new light on what is happening with my NPT

View this message in context: http://gromacs.5086.n6.nabble.com/Diatomic-in-MeCN-NPT-NH-and-PR-simulation-segfaults-after-1-us-tp5001845p5002696.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.

More information about the gromacs.org_gmx-users mailing list