[gmx-users] Re: animating normal modes

[Graham Smith]

> does anyone know a software which can be used to animate normal
> modes, display Cartesian displacement vectors...? Thanks. 

I think what you want can be done with 
g_anaeig -extr  and vmd.  

e.g. for first principal component (I presume normal modes will be 
the same) ,
g_anaeig -first 1 -last 1 -v eigenvec.trr -s sim.tpr -f sim.xtc \
 -extr extreme_1.xtc -nframes 20  

Then make a .gro file of the subset of the atoms that were used
in the pric cpts analysis, and read the gro and extreme_1.xtc 
into vmd. Animate with the "rock" option looks nice. 

If you havent got vmd, you can use ngmx, but that needs a tpr
for the right subset of atoms, which can be made with tpbconv. 
(I once wrote a program that interpolated back missing atoms in
the case that princ components had been done on e.g. ca atoms only,
but it's not in working order for gromacs 3 I'm afraid) 

The displacement vectors are in the eigenvec trr so you can look
at them with rasmol (etc) if you convert them to pdb format 
with sthg like 
trjconv -f eigenvec.trr -s struc.pdb -o displ_1.pdb -dump 1 
for the first evec etc  (-dump 0 gives you the protien structure
again) 

Graham 

########################################################################

Dr. Graham R. Smith,
Biomolecular Modelling Laboratory,
Cancer Research UK,
44 Lincoln's Inn Fields,
London WC2A 3PX,
U.K.
Tel: +44-(0)20 7269 3348
email: graham.smith at cancer.org.uk
URL: http://www.bmm.icnet.uk/~smithgr