Aaron Fafarman wrote:
Hello,
Thanks for reading this. I'm doing many-nanosecond simulations (GMX
3.3.1) with a 2 fs time step and I would like to analyze every single
frame (or at minimum every tenth frame) of the trajectory for the
presence of a hydrogen bond to one particular atom in the simulation.
The problem with doing the analysis after the trajectory is completed
is that the trr or xtc file would contain many millions of structures
and therefore be way too large to store on our cluster even
temporarily.
One solution I can imagine but don't know how to implement is to have
g_hbond continuously process the trajectory file, printing the h_bond
analysis for each new coordinate set and then erasing (or never
storing) the previous coordinates. Does anyone know of an
implementation of this, or a better way to achieve a frame-by-frame
h-bond analysis? Perhaps there is a simple unix-based file-system
approach to this (maybe using tempnam)? Thanks in advance.
First I'd question whether the frame-by-frame analysis was statistically
able to tell you anything. Successive MD or MC frames are not
independent, so a trajectory of N steps can't give anything like N
independent samples from an ensemble.
Next, it would be straightforward to partition the calculation into
manageable chunks, do the analysis after each chunk was complete and
then use trjconv to reduce the amount of data you wish to store before
continuing the calculation.
Obviously, you should consider your values of nstxout, nstvout,
nstenergy, nstxtcout and xtc-groups carefully in advance. See the wiki
page about restarts.
Mark
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