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

[Dries Van Rompaey]

Hi,

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:
https://www.google.be/url?sa=t&source=web&rct=j&url=http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2872215/&ved=0ahUKEwjq3I7M-YbMAhXI_w4KHQeeCX8QFggoMAU&usg=AFQjCNHnkqQys4V7UYCURTPZyKQEYrGdWQ&sig2=rpmfKD8E07TCQ_XfeUyE3Q
It might be worth looking into their methodology.

Good luck

Dries
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:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/02_topology.html
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
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