Re: [GaMD-discuss] PyReweighting-2D

[Miao, Y. <Yin...@me...>]

Hi Tushar,

We have new GaMD tutorials that cover setting simulation input parameters and free energy calculations: https://www.med.unc.edu/pharm/miaolab/resources/gamdtutorials/. Hope you can find them helpful, especially with igamd=3 simulations in the starting GaMD tutorial.

Best,
Yinglong

Yinglong Miao, Ph.D.
Associate Professor
Department of Pharmacology and
Computational Medicine Program
University of North Carolina - Chapel Hill
Tel: 1-919-962-5696
http://miaolab.org

Editor-in-Chief
npj Drug Discovery
https://www.nature.com/npjdrugdiscov

On Oct 10, 2025, at 3:41 AM, TUSHAR GUPTA via GaMD-discuss <gam...@li...> wrote:

Hello community
I am new to GAMD and WHAM. I have to run reweighting of my GAMD results for free energy landscape analysis. I used the PyReweighting-2D file from the Miao lab for the same.
This is the code I ran for GaMD analysis in AMBER,
&cntrl
  imin=0,irest=1,ntx=5,
  nstlim=250000000,dt=0.002,
  ntc=2,ntf=2,ig=-1,
  cut=10.0, ntb=1, ntp=0,
  ntpr=25000, ntwx=25000, ntwr=25000
  ntt=3, gamma_ln=2.0,
  temp0=300.0,ioutfm=1,iwrap=1,
  igamd = 3, iE = 1, irest_gamd = 0,
  ntcmd = 1000000, nteb = 1000000, ntave = 50000,
  ntcmdprep = 200000, ntebprep = 200000,
  sigma0P = 6.0, sigma0D = 6.0,
  ethreshd = 4848.53, alphad = 231.2
  ethreshp = -827.93 alphap = 5345.28
 &end
<image.png>
I got the following graph, it is correct. I want to zoom to the desired region and change the background to white. Are there any updated input files that I need to use? And please suggest commands that I need to use to run the free energy landscape.
The help would be highly appreciated.
Thank you
Tushar Gupta
PhD scholar
Bennett University

“Knowledge which is acquired under compulsion obtains no hold on the mind.” – Plato
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