[gmx-users] grompp -r again

[hugo verli]

The energy minimization gives the boat conformation and the energy terms for
improper angles and bonds are close to 0. So what paramters can I change to
obtain the boat conformation in a FEP calculation? The simulation time of each
lambda step? The size of the lambda step?

Hugo Verli.


> Try to do an energy minimization of the molecule and see what the
> minimum looks like. If all is well your molecule should become a boat
> and the energy terms for improper angles and bonds should be small. If
> you don't get a boat something is wrong with your topology. You could
> try to increase the number of exclusions so that no intramolecular Van
> der Waals interactions are calculated.
> 
> 
> -- 
> 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://xray.bmc.uu.se/~spoel
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