[gmx-developers] Linear bond angles= exploding energy

David van der Spoel spoel at xray.bmc.uu.se
Wed Apr 1 21:17:12 CEST 2009

Paul Whitford wrote:
> I wasn't sure if I should post this to the gmx-users or gmx-developers list.
> I am constructing coarse-grained CA models for proteins.  Adjacent CA 
> atoms are connected by harmonic bonds and sets of three CA atoms are 
> connected by harmonic angles.  I have noticed that when a bond angle 
> gets linear (pi) , there is a large spike in the potential energy and 
> that part of the system goes  a bit wild (unrealistic high 
> accelerations).   I suspect this has to do with the dihedral term, but 
> I'm not sure.  In Amber, there was a comment about a disconinuity when a 
> dihedral has a linear angle (I can't find it at the moment).  Was this 
> considered when writing gromacs?   In all-atom simulations, this is not 
> be a problem, but in these coarse grained methods linear angles are ok, 
> since they are not "real" covalent bonds.   Any thoughts/fixes would be 
> appreciated.

You did not state which version you have. The problem is in the angle 
terms,not dihedrals, but it has been fixed (or diminshed) in gmx 4.x . 
Question is whether you really need angles, maybe you can use a 
nonbonded term instead?
> Thanks
> -Paul
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David van der Spoel, PhD, Professor of Biology
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://folding.bmc.uu.se

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