[gmx-users] poly(lactic acid) .itp or .top file

David spoel at xray.bmc.uu.se
Sat Aug 31 08:51:22 CEST 2002

On Fri, 2002-08-30 at 23:42, Erik Lindahl wrote:
> Improper dihedrals are more or less intelligent guesses in most 
> forcefields I know of :-) Check the values in the gromacs and gromos 
> forcefields and pick something (OPLS does it slightly different since
> the use a periodic cosine). If you make it way too low it won't have
> any effect, and if you pick it way too high the molecule might slightly 
> be too rigid.
If you make the fc for impropers too high, you may also introduce
non-physical high frequency vibrations that may destabilize your
simulation. Just stick to one of the two values in GROMOS (40 kcal or 80
kcal) and test whether the fluctuations are within bounds after
averaging over your simulation. 

> Cheers,
> Erik
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Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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