[gmx-users] grompp -r again
hugo at acd.ufrj.br
Thu Oct 3 17:40:37 CEST 2002
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?
Besides the two conformations coexist in solution, so the energy barrier between
them should not be soo high.
> On Thu, 2002-10-03 at 15:46, hugo verli wrote:
> > Hi,
> > I know that grompp can take an extra coordinate file for the
> > positions using the option -r. I want to use this option to convert a
> > 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
> > conformational state, but I cannot see this conformational change in a
> > timescale. Should the -r option work with ring conformational
> you probably need even higher force constants. What you could also do
> 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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