On 8/8/12 11:25 AM, Asaf Farhi wrote:
Dear Justin
Thank you very much for the reply.
I want to understand how to calculate binding free energy difference of both
molecules to another molecule.
So do I have to use dummy atoms, meaning that there won't other forces besides
the bonding term?
I'll look at the examples.
Yes, bonded terms can and will be different. Start with a very simple example,
like methane to ethane, before diving into your more complex system. Follow the
logic in the example in section 5.7.4 in creating your topology.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Only plain text messages are allowed!
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
* Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
