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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Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
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