VMD-L Mailing List

From: Lubos Vrbka (lists_at_vrbka.net)
Date: Sun Aug 20 2006 - 11:27:19 CDT

alexandra.marques_at_fc.up.pt wrote:
> Hi
>
> I want analyze my mdcrd trajectory with some Tcl scripts, namely, calculate the
> rmsd for individual residues using the residue_rmsd.tcl script. However my
> trajectory is large and when I start the calculation vmd crashes. Is there any
> easy way to analyse large mdcrd files from amber?
maybe you just don't have enough memory to load your trajectory?

i would suggest the following

1) strip waters from your trajectory (it can save considerable amount of
space and make your analyses much faster. of course, in case you need
the waters there for the analysis, this doesn't apply), you can do it
using ptraj
2) try again in vmd. the other option - why not use ptraj again? it is
capable of calculating per-residue rms, iirc.

regards, 

-- 
Lubos _@_"
http://www.lubos.vrbka.net