[gmx-users] Parallel do_dssp analysis over mpi?

[Mark Abraham]

On 9/11/2010 6:24 AM, Ali Naqvi wrote:
> Dear All,
> I have a trajectory of 100ns and have been trying to analyze it using 
> dssp program. I guess this question also goes for other analysis 
> programs like g_rama, g_rdf and what not.
>
> Since the trajectory is big, it takes hours to analyze with do_dssp.. 
> infact 48 hours. I have been able to analyse only one set of 100ns and 
> have 7 more trajectories. Is it possible to get it running in parallel 
> to expedite the analysis? If so, which flags need to be appended?

Almost certainly you do not need to analyze every snapshot in a 100ns 
trajectory. Neighbouring frames are highly correlated and you do not 
gain significant new information. I'd be using -dt to analyze only every 
nanosecond or 100ps or something. (And when asking for help, I'd be 
providing my command line so that people know whether you're doing 
something like this, and information about the trajectory you're 
analyzing...)

Mark