[gmx-users] Position restraint problem

Mark Abraham 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 

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