[gmx-users] strange new H-H bond formation during MD

Stéphane Téletchéa steletch at jouy.inra.fr
Mon Oct 23 15:25:29 CEST 2006

Qiao Baofu a écrit :
> Hi Mark,
> Thanks for your reply.
> I used these:
>   1. vmd em_out.gro 
>   2. use the "load data into molecules...", select md1.trr, and then load
>   3. when the anmination is finished, I can see some H-H bonds.

As already stated by Mark, VMD calculates by its own bonds, so i won't 
be too much bothered if he fails in displaying bonds. Remember vmd is 
just *displaying* them, not actually doing any calculation on it (which 
gromacs does).

If you really want to see if the bond is involved in any sort in your 
calculation, you should monitor it with gromacs and/or vmd (plot the 
bond versus distance while using vmd, both use xmgrace in the end).

BTW, you could use my modified graphlabel.tcl routine to display atom 
names under vmd + xmgrace:




Stéphane Téletchéa, PhD.                  http://www.steletch.org
Unité Mathématique Informatique et Génome http://migale.jouy.inra.fr/mig
INRA, Domaine de Vilvert                  Tél : (33) 134 652 891
78352 Jouy-en-Josas cedex, France         Fax : (33) 134 652 901

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