[gmx-users] How to simulate broken and movement of molecules
albert_sun9 at yahoo.com
Mon Nov 17 19:26:01 CET 2003
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.
I still need your help
How can we see the broken molecules? when apply surface-tension or pull force?
Anton Feenstra <feenstra at chem.vu.nl> wrote:
Albert Sun wrote:
> Hi, Dear users,
> If I have a group of molecules, and an anisotropic pressure or surface_tension is applied to the group of molecules. It will be broken when the forced reach certain value, and we should see the separation on screen of atoms.
> However, what I noticed is: the atoms are continually moving in a direction, no broken and no separated movement of atoms can be viewed.
> Would appreciate if you could highlight me on this.
First thing I could think of is that separation may only occur at (much?)
longer timescales than that you are simulating and looking at.
Second, I can imagine that depending on the size of your system, it could
have different behaviour. E.g. the separation you expect may actually be
unfavourable for a 'small' system size, take for example that a box of
(spc) water in an MD simulation will not boil when the temperature is raised.
| | |
| _ _ ___,| 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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