VMD-L Mailing List

From: Per Jr. Greisen (greisen_at_binf.ku.dk)
Date: Thu Mar 15 2007 - 14:14:20 CDT

Hi,

1. Is there an easy way to get the average structure from a MD simulation
using VMD?

My alternative is to get all the coordinates (aligned for each frame) and
make a script of my own in order to generate an average structure. Just to
make sure when one use the python command align() in a loop over all the
frames - e.g

for i in range(k):
    cas = sel.AtomSel('protein')
    cas.frame(i)
    cas.align()

one gets the coordinates with the least difference?

I have a last question regarding the use of BigDCD - I would like to get
my coordinates out from a MD simulation where the size of the DCD-file
exceeds my physical RAM:

import Molecule as mol

m = mol.Molecule()
m.load('protein.psf')
m.load('min_prot.dcd')

is it possible to include the bigDCD into the python mode?

Thanks in advance 

-- 
Best Regards
Per Jr. Greisen