[gmx-users] image jumps in VMD

[Graham Smith]

> I use vmd_1.72 to visualize gromacs md trajectory using "animate". 
> 1. Frequently the image jumps between edges and goes out of visible
> screen window

how about 

trjconv -s ok.pdb -f input.xtc -o output.xtc -pbc nojump

This fixed a similar problem I had with vmd with a multichain protein; 
some subunits would flicker across the pbc and others not. The -s file
that you use should have the protein how you want it. 

I imagine that the output trajectory might be dodgy for calculating
things like water diffusion coefficients. 

It seems that the decision about where to put a molecule/chain in
relation to the pbc is made using one end of the chain rather than its
Centre of Mass? 

-G

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Dr. Graham R. Smith, 		       Department of Biological Sciences,  
Biomolecular Modelling Laboratory,     Biochemistry Building,              	
Cancer Research UK, 		       Imperial College of Science,        	
44 Lincoln's Inn Fields, 	        Technology & Medicine,             	
London WC2A 3PX,		       London SW7 2AZ,                     	
U.K. 				       U.K.                                	
Tel: +44-(0)20 7269 3348 	       Tel: +44-(0)20 7594 5737            	
email: graham.smith at cancer.org.uk	
URL: http://www.bmm.icnet.uk/~smithgr