# [gmx-users] Question about gmx bar

Justin Lemkul jalemkul at vt.edu
Wed Feb 28 00:33:03 CET 2018

On 2/27/18 6:31 PM, Thanh Le wrote:
> Hi Justin,
> I assume, in order to get Coulomb energy for the first 10 stages, I should change coul-lambdas stages to the same row as bonded-lambdas (0.0 0.01 0.025 0.05 0.075 0.1 0.2 0.35 0.5 0.75 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.0 1.0 1.0 1.0 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0).
> Is there another way to do it? Is there a paper I can read to get more details about the subject?

No, but there's a tutorial:

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

And other material on, e.g. alchemistry.org.

-Justin

> Thanks,
> Thanh Le
>
>
>
> On 2/27/18 4:13 PM, Thanh Le wrote:
>> Hi everyone,
>> I just finished running 2 sets of simulations (ligand in water and RNA+ligand in water) for my system to learn about its binding energy. Using the parameter for BAR method, I ran 20 simulations for ligand in water and 30 simulations for RNA+ligand in water with different lambda stages. What is interesting/confusing to me is the 0 energy from stages 0-10. Based on what I have been reading and the set up of my prod.mdp, these stages should give Coulomb Energy. If you can tell me why or how to fix it, I would greatly appreciate your help.
> You've defined only a bonded transformation in those stages:
>
> bonded-lambdas           = 0.0 0.01 0.025 0.05 0.075 0.1 0.2 0.35 0.5 0.75 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.0 1.0 1.0 1.0 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0
> coul-lambdas             = 0.0 0.00 0.000 0.00 0.000 0.0 0.0 0.00 0.0 0.00 0.0 0.25 0.5 0.75 1.0 1.00 1.0 1.0 1.0 1.0 1.0 1.0 1.00 1.0 1.00 1.0 1.00 1.0 1.00 1.0
> vdw-lambdas              = 0.0 0.00 0.000 0.00 0.000 0.0 0.0 0.00 0.0 0.00 0.0 0.00 0.0 0.00 0.0 0.05 0.1 0.2 0.3 0.4 0.5 0.6 0.65 0.7 0.75 0.8 0.85 0.9 0.95 1.0
>
> Your electrostatic terms remain in state A (lambda = 0) and there is no difference in bonded energies, so the first windows are essentially doing nothing.
>
> -Justin

--
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==================================================