[gmx-users] Fwd: free energy calculation.

[Dallas Warren]

Can't help directly, but ....

Good primer for doing Gibbs energy calculations and list of references
on to read further you can find at :

http://www.alchemistry.org/wiki/Main_Page

Other place you should be looking is the literature, what have others
done and published when doing what you are doing?

Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren at monash.edu
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.



On Tue, 28 Aug 2018 at 09:38, neelam wafa <neelam.wafa at gmail.com> wrote:
>
> Hi everyone.
> Kindlt need your help urgently.
>
> ---------- Forwarded message ---------
> From: neelam wafa <neelam.wafa at gmail.com>
> Date: Mon, 27 Aug 2018, 3:41 pm
> Subject: free energy calculation.
> To: <gmx-users at gromacs.org>, <gromacs.org_gmx-users at maillist.sys.kth.se>
>
>
> Hi!
> Dear gmx users,
> I have md simmulations of a protein with four different ligands. now I want
> to calculate the free energy of binding. which method does suit after md
> simmulation?  either g_mmpbsa or gmx BAR  method.  If I use BAR method is
> it necessary to set charges to zero as in the tutorial given at
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/03_workflow.html.
>
> I s necessary to turn off couloumb interactions for calculating free energy
> of ligand protein complex. if i want to use coloumb interactions also then
> should i set the
>
> coul_lambdas values in the same way as vdw_lambdas.
>
> Another question is that there is another tutorial available at
> http://www.gromacs.org/@api/deki/files/262/=gromacs-free-energy-tutorial.pdf
>
> In this tutorial the system has been equilliberated before generating
> the lambda states.
>
> while in the justin tutorial each lambda state is equiliberated separately.
>
> kindly tell me which one is more suitable for a protein ligand complex.
>
> looking forward for your cooperation.
>
> sorry if the questions are trivial.
>
> Regards
>
> Neelam
>
> Ph.D scholar
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