Talk:Mod:Hunt Research Group/VmdBonding

Bonding in VMD

problems with bonding under PBC

• does your file load with bonds stretching across the screen?
• this is a common issue with VMD

• turn on dynamic bonds

GRAPHICS:Drawing Method:DYNAMIC BONDS

modify the bond cut-off so that bonded molecules are bonded

then reduce the bond radius to more stick like structure

good options are bond radius 0.1 and the distance cut-off 1.4

• at the same time add VDW spheres on the atoms to help mimic a CPK look

add representations for each of the atom types

for example element O H

now use VDW for the O and H atoms and turn down atom radius 0.2 or 0.3

for other atoms such as a Cl anion you will want a larger radius say 0.4

TOPO package

• another option for dealing with too many bonds is to use topo

topo readvarxyz filename

topo clearbonds all

topo retypebonds all

topo guessbonds all