[gmx-users] (no subject)

gmx-users-admin at gromacs.org gmx-users-admin at gromacs.org
Tue Oct 29 04:13:58 CET 2002

On Wed, 2002-10-23 at 16:05, hugo verli wrote:
> David,
> I follow your suggestion to use free energy perturbation to transform one
> conformation in another conformation. I fix the boat conformation using improper
> dihedrals.
> 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?
Try to do an energy minimization of the molecule and see what the
minimum looks like. If all is well your molecule should become a boat
and the energy terms for improper angles and bonds should be small. If
you don't get a boat something is wrong with your topology. You could
try to increase the number of exclusions so that no intramolecular Van
der Waals interactions are calculated.

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://xray.bmc.uu.se/~spoel
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