,
Hannes.
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
[gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of
Julian Zachmann [frankjulian.zachm...@uab.cat]
Sent: 29 July 2015 14:10
To: gmx-us...@gromacs.org
Subject: [gmx-users
Dear Gromacs-Users,
I calculate relative binding energies using free energy perturbation (FEP)
and mbar. I have the binding data for 4 receptors and two ligands which are
almost identical. The only difference is the change from a methyl group to
a hydrogen. I alchemically convert a methyl group
...@maillist.sys.kth.se
gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Julian
Zachmann frankjulian.zachm...@uab.cat
Sent: Wednesday, July 15, 2015 9:20 AM
To: gromacs.org_gmx-users@maillist.sys.kth.se
Subject: [gmx-users] Free energy calculations (FEP) and soft core
potential 1-1-48
Dear Gromacs Users,
I am running free energy calculations (FEP) to estimate relative binding
affinities. So far, my results don't match the experimental results (not
even close), so I must be doing something wrong.
My protocol is the following:
- Energy minimisation
- Leap frog minimisation
-
/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.
--
Julian Zachmann
Laboratori de Medicina Computacional
Unitat de Bioestadistica. Facultat de Medicina
Universitat Autonoma de Barcelona
08193 Bellaterra (Barcelona). Spain
Phone: (3493) 581 2797
Fax: (3493
...@stfc.ac.uk:
On Tue, 19 May 2015 17:48:17 +0200
Julian Zachmann frankjulian.zachm...@uab.cat wrote:
Concerning the changes of the atom types: the changes in the charges
are really small and the results will probably be the same if I would
not convert the whole ligand, just the 4 atoms
