VMD-L Mailing List

From: Bogdan Costescu (bcostescu_at_gmail.com)
Date: Thu Nov 10 2011 - 08:20:41 CST

On Wed, Nov 9, 2011 at 21:41, Aleksandr Kivenson <kivenson_at_brandeis.edu> wrote:
> The problem with this approach is that VMD apparently reads .trr files from the
> very beginning every time this command is called

It's not a problem with VMD. The GROMACS file formats .xtc and .trr
are not supposed to be used for random access (= jumping to a
particular frame); you can check out xdrfile, a library provided
together with GROMACS for accessing their trajectories. If the access
is done such that the parts are not overlapped, then you could do the
reading of a part, process it, then proceed with reading for the next
part, such that the frame accesses are optimized.

Cheers,
Bogdan