[gmx-users] grompp -r again

[David van der Spoel]

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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