On 11/5/12 11:25 PM, benjfitz wrote:
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
simulations?
The fact that any system crashes at 1.07 us (either CS2 or MeCN) suggests that
the problem is external to your molecule's topology. It seems too coincidental
that the times are the same, almost as if your system is running out of memory
or there is some nefarious error accumulating a problem. Unfortunately, I
suspect this will be really hard to debug, especially given the fact that it
takes a very long time for the error to occur. If you're interested in trying
to debug it yourself, change algorithms one by one, i.e. tcoupl and pcoupl
methods, and see if the situation improves. This may not be how you want to do
your data collection, but it would either rule out or identify which algorithm
might be failing.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
