[gmx-users] grompp -r again

David spoel at xray.bmc.uu.se
Thu Oct 3 18:55:02 CEST 2002

On Thu, 2002-10-03 at 17:40, hugo verli wrote:
> Thanks, David.
> But I am using for now a system of just one sugar ring to test the conversion.
> However, I need to apply this transformation to a polyssacharide system
> complexed to one protein, so the system syze will became prohibitive to free
> enegy perturbation, dont'it?
Not necessarily. If you only want to modify a single ring in the whole
sugar chain it should still work, at least if the binding mode remains
the same.
> Besides the two conformations coexist in solution, so the energy barrier between
> them should not be soo high. 
Well, that both exist means that the free energy difference is not very
large; the barrier may be in principle, although it doesn't seem too
likely in this case.

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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