[gmx-users] grompp -r again
hugo at acd.ufrj.br
Fri Oct 4 19:40:27 CEST 2002
I'm trying to follow your suggestion David, so I'm reading about performing free
energy perturbation in gromacs.
I understood from the manual that all the structure transformations on this
calculation are determined in .top and .mdp files, is it correct?
If it is correct, how can I transform one conformation in another? The topology
will be the same for the two conformers and the only modification occurs in the
system coordinates... Am I missing something?
Thanks a lot for your help,
> 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
> > However, I need to apply this transformation to a polyssacharide
> > 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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