I'm a little late to the discussion as I've been on the road, but that
won't stop me from throwing in my (late) two cents.
On the issue of a new inpcrd/restrt format that can support 1M+ atoms,
what about using the NetCDF trajectory format? As I see it, some
advantages are (some of these may not be benefits relative to amoeba
format; I'm not familiar with its particulars):
* we already have full support in ptraj and VMD
* sander and pmemd would require some "plumbing" work, but most of the
needed code is already there
* *leap doesn't know how to speak NetCDF, but it's a pretty
straight-forward API, probably easier than having to write to a new file
spec
* performance and filesize benefits
* It's an extensible format so further down the road things like
constant pH that currently require separate restart files might be
folded in.
Some thoughts on how the interface might work: To avoid adding yet
another flag to mdin, we could detect the format of the inpcrd file and
write restarts in the same format. If we default to using data from the
last frame of NetCDF inpcrd files, then you could restart a run directly
from the trajectory file of the previous run without having to process
it through ptraj. In some cases this might even eliminate the user's
need for a separate restart file.
It appears that we have (wisely, I think) decided not to implement any
of this in time for 10, so we have some time to work it out. What do you
all think? If people like the idea, I'll volunteer to do the
implementation in sander.
John
Received on Sun Dec 16 2007 - 06:07:08 PST
