Hi all,
I am running umbrella sampling simulations with the NCSU PMD module and
want to extend my analysis beyond the small number of order parameters that
I saved during the simulation. For example I'd like to look at solvent
distributions near my active site. To do this I obviously need to use
ptraj or some other program to extract additional time series data.
However, I had difficulty getting the time series from the NCSU module and
those extracted sander mdcrd files to line up/be the same size. I believe
the "offending" behavior is as follows:
- sander begins writing trajectory frames after ntwx steps, that is:
frame1 = ntwx and frameN = nstlim for a total of N = (nstlim/ntwx) frames
(assuming nstlim mod ntwx = 0)
- the NCSU modules begin writing frames immediately, that is: frame1 = 0
and frameN = (nstlim - output_freq) for the same total of N steps (assuming
ntwx = output_freq)
The result is that the reading frame is off between the two time series
types. If you want a properly synced time series you would have to discard
the first step from NCSU and the last step from sander, which diminishes
the data to N - 1 points. Although obviously I can easily remedy the whole
situation by extracting all of my time series' from the mdcrd files, it
would then seem silly to even print the NCSU output in the first place.
Does anyone else find this behavior strange? Should it be changed?
Regards,
Brian
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Wright-Rieman Hall 101
Graduate Program in Chemical Physics : 610 Taylor Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
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Received on Wed Nov 09 2011 - 07:00:06 PST
