VMD-L Mailing List

From: Christopher Gillespie (gillescche_at_gmail.com)
Date: Fri May 23 2008 - 18:43:22 CDT

Hello all,
I have been searching through the lists looking for an answer to this. I
want to get the gofr for the ions in my system relative to specific parts of
my protein, which I can do perfectly fine with my small systems. On my
systems approaching 100k atoms the dcd files are on the order of 18-20GB.
 So I break these up into 4 smaller dcd files and try to load the dcd but it
is still to big to load directly. I thought about using bigdcd for this but
I am not sure how a gofr calc would get handled since the examples of COM or
RMSD do not require knowledge of the counts from each previous frame.

Is there a way to either use bigdcd with gofr or combine gofrs from smaller
dcd files to make a gofr for the entire run?

So far I break it down to 1ns parts for a 4ns production run, but that is
still too large.

Thanks

Chris