[gmx-users] intramolecular /intermolecular forces

David van der Spoel spoel at xray.bmc.uu.se
Tue Nov 29 09:11:24 CET 2005

Sven Huttenhouse wrote:
> Hello all.
> In my simulation I'm only interested in the intermolecular forces and 
> not the intramolecular force. I'm trying to simulate the crystallization 
> of Glycine and I'm interested in getting clusters out of my solution. 
> I'm only interested in how the molecule will interact with each other 
> (non bonded interaction).
> How can I elliminate the intramolecular interaction?
> I tried to set the (nrexcl=0) but the system didn't work. did I do the 
> right thing?
No, this will explode your molecules, check ch.4 in the manual.
If I recall correctly you have 200 GLycines in solution, in principle 
yuo can define 200 different energy groups (+ solvent and/or ions) and 
then you will get a huge energy file from which you can extract all the 
interaction energies.

> Kind regards
> Sven
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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