[gmx-users] Position restraint problem
Mark.Abraham at anu.edu.au
Sun Jan 16 20:43:21 CET 2011
On 17/01/2011 6:25 AM, Marcelo Silva wrote:
> Hello everybody,
> I tried to run a simulated annealing protocol with 500 molecules of
> perfluorohexane, trying to optimize their structure and keep on with
> further equilibration.
> Since in the end of simulated annealing there were a lot of holes in
> the NPT box, I've now tried to restrain the positions of the
> perfluorohexane molecules using -DPOSRES (I've attached the mdp file).
Sounds like you might need to check out FAQ #11.
> The problem is that mdrun keeps running in background but there's no
> output showing in the sa.log file. What could be the problem?
File systems store I/O in temporary areas in memory, and only write
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the gromacs.org_gmx-users