Dear Gromacs users! I wonder does it exist somewhere a full description (in 
manual, tutorial...) how to calculate free energy using Umbrella sampling, for 
example, for ligand-receptor dissociation? I read the manual but I am not sure 
that I understood it completely.
Is it necessary to specify coordinates of the ligand position outside the 
receptor binding pocket (to which the dissociation should lead)? 
How is it possible to specify the correct direction of ligand movement?
Should I make one md stimulation of the system for one ligand position or 
several for different lambda (from 0 to 1) that describes the changing of its 
position? Or maybe this refers only to TI method?
Thanks,

Alexander 
_______________________________________________
gmx-users mailing list    gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

Reply via email to