[gmx-users] Preparing dual topology for free energy calculation

Dries Van Rompaey dries.vanrompaey at gmail.com
Mon Apr 11 22:28:57 CEST 2016


I'd recommend alchemistry.org as a good place to start. Justin's tutorial
(the one you linked to) is an example of an equilibrium free energy method,
not a slow growth method. As a general rule, equilibrium methods are easier
to use and are recommended for people without extensive experience.

The following paper did something similar to what you're looking to do:
It might be worth looking into their methodology.

Good luck

On 11 Apr 2016 5:41 p.m., "Tushar Ranjan Moharana" <
tusharranjanmoharana at gmail.com> wrote:

Hi everyone,
I want to calculate difference in folding free energy due to certain
mutations. I want to follow the slow growth method as mentioned in:
However I don't know how to prepare dual topology (even after reading
manual, section  5.7.4). I want to use gromos 53a6 force field. Can anyone
tell me how to prepare dual topology. Any link to read or tutorial will be
of great help.

Thanks a lot for the help.

"A society with free knowledge is better than a society with free food"

Tushar Ranjan Moharana
B. Tech, NIT Warangal
Ph D Student, CCMB
Gromacs Users mailing list

* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send
a mail to gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list