[gmx-users] shells and VdW interactions

David spoel at xray.bmc.uu.se
Sun Feb 15 07:31:01 CET 2004

On Sun, 2004-02-15 at 02:34, Stefano Piana wrote:
> I am currently running shell MD in an ionic crystal and with version 3.2 
> it runs fine, however for my system I have to use a rather small 
> timestep to keep energy conservation.
> I would like to ask if anybody knows if it is possible to put a Buck 
> potential on the shells and how is this accounted for in terms of 
> exclusions.
exclusions have to be given manually, e.g.
[ exclusions ]
; >From atoms
1	3 	4	 5

There is no Buckingham 1-4 if I'm not mistaken...

> Can I define pairs between shells and shells and/or between shells and 
> atoms?
> With version 3.2 the buckingham potential seem tu work fine, however
> I observe a weird behaviour when I try to build pairs with a Buckingham 
> potential; although my C term of the Buckingham is 0 the total 1-4 
> interaction energy is large and negative (!!). Furthermore I observe 
> that after a few steps the 1-4 interacting atoms collapse and the system 
> blows up.
Check what you have in your tpr file, with:
gmxdump -s topol.tpr | more
and then look for "idef" (no quotes) there you will see the parameters
etc. Maybe you pairs are misinterpreted as lennard jones...

> I did not have time to check throughly all the numbers but it looks to 
> me as if there is some kind of sign problem in the creation of the 
> pairs; as a crosscheck I changed the sign of the 1-4 scaling factor to 
> negative and now the simulations runs fine (Although I would not trust 
> the results at all...).
> Suggestions? Comments?
> Bye,
> Stefano
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David van der Spoel, PhD, Assist. 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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