[gmx-users] grompp -r again

hugo verli 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,

Hugo Verli.

> 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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