[gmx-users] (no subject)

[gmx-users-admin at gromacs.org]

The energy minimization gives the boat conformation and the energy terms for
improper angles and bonds are close to 0. So what paramters can I change to
obtain the boat conformation in a FEP calculation? The simulation time of each
lambda step? The size of the lambda step?

Hugo Verli.


> 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
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
> 
_______________________________________________
gmx-users mailing list
gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-request at gromacs.org.