[gmx-users] grompp -r again
hugo at acd.ufrj.br
Wed Oct 23 16:05:46 CEST 2002
I follow your suggestion to use free energy perturbation to transform one
conformation in another conformation. I fix the boat conformation using improper
To test if these improper works I simulate a chair conformation with the boat
topology and the transformation occur quickly, in a 50ps simulation. So I go to
the FEP calculations, using Dlambda step of 0.05 for 50ps. However in the end of
the simulation I did not obtain the the boat conformation. The ring adopt a
distorted conformation very different from the intented boat conformation.
Did you understand what is happening? Am I doing something wrong? I tested
different combinations of improper dihedrals and I see the same profile. How can
I fix it?
Many thanks in advance,
> 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
> gmx-users mailing list
> gmx-users at gromacs.org
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users