[gmx-users] HYP GROMOS

David van der Spoel spoel at xray.bmc.uu.se
Sun Oct 19 10:52:13 CEST 2008

Abil Aliev wrote:
>   Hello,
> I have done calculations using standard GROMOS 43a1 and 53a6 parameters 
> (GROMACS 3.3.3) for a 4-hydroxy-L-proline derivative (HYP), where the 
> gamma-OH and the alpha-CO groups are trans to each other in the starting 
> structure. However, over the course of MD the trans-configuration of 
> these two substituents changes into a cis-configuration, which was not 
> supposed to happen. Is there any way to avoid such isomerisation?
Dihedral potentials, maybe you need to add an improper...
> Abil
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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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