Dear Justin Thank you very much. I really appreciate it.
Best regards, Asaf ________________________________________ From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf of Justin Lemkul [jalem...@vt.edu] Sent: Wednesday, August 08, 2012 9:35 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Question about Thermodynamic Integration 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 -- 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
