[gmx-users] How to simulate broken and movement of molecules

Albert Sun albert_sun9 at yahoo.com
Wed Nov 19 19:59:01 CET 2003

Dear Anton and users,
When we simulate molecules under force, is it possible to set a distance limit such as a spring?, once the limit between two ends (atoms)  is reached, the spring will broken and two ends(atoms)  will separate and move in opposite direction.
( sorry, I am in mechanical area and please forgive me to raise the stupid inquiry)
In VMD, I only can view the structures of molecules, but could not see the broken and opposite movement.

Anton Feenstra <feenstra at chem.vu.nl> wrote:
Albert Sun wrote:
> Thanks, Anton and users,
> I understand this should reply on time scale and size, also forces applied, but
> I tried a few examples and could not see how those atoms are broken and separated.

You can try e.g. g_rdf to get an overall picture of molecule packings,
or you could inspect 'visually' using a trajectory viewer (e.g. ngmx or
vmd), or look at snapshots (e.g. load a pdb file in rasmol).

By the way, atoms are not likely to break... Also, molecules will not
break in MD, but they may separate... ;-)


_____________ _______________________________________________________
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 |
| | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/ |
| | "If You See Me Getting High, Knock Me Down" |
| | (Red Hot Chili Peppers) |

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