[gmx-users] grompp -r again

David van der Spoel spoel at xray.bmc.uu.se
Thu Oct 3 15:50:01 CEST 2002

On Thu, 2002-10-03 at 15:46, hugo verli wrote:
> Hi,
> I know that grompp can take an extra coordinate file for the restraining
> positions using the option -r. I want to use this option to convert a 6-member
> ring from a chair conformation to a boat conformation. The system (ring plus
> water) is equilibrated in a chair conformation. I have a boat conformation in
> water. I'm trying to use -r boat.gro to drive the chair.gro to a less stable
> conformational state, but I cannot see this conformational change in a 500ps
> timescale. Should the -r option work with ring conformational behaviour?
you probably need even higher force constants. What you could also do is
use free energy perturbation. It will give you an estimate of the free
enery of the transition...

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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