Re: [gmx-users] AWH with two bias potentials

To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] AWH with two bias potentials Thanks a lot for all the helpful information, I will decrease the initial error and increase the diffusion. Actually before seeing your email I had modified my .mdp file like this, which made mdrun behave

Re: [gmx-users] AWH with two bias potentials

mdrun behavior. Berk From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Cédric Leyrat Sent: Thursday, February 14, 2019 9:00 PM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] AWH with two bias potentials awh

Re: [gmx-users] AWH with two bias potentials

, February 14, 2019 9:00 PM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] AWH with two bias potentials awh = yes awh-nstout = 1 awh-nbias = 1 awh1-ndim = 2 awh1-dim1-coord-index = 1 awh1-dim1-start

Re: [gmx-users] AWH with two bias potentials

14, 2019 9:00 PM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] AWH with two bias potentials Thanks Berk, What you're saying makes perfect sense. I should be using one 2D bias instead of two 1D biases. And I should use a cutoff on the free energy. This way gmx awh should

Re: [gmx-users] AWH with two bias potentials

in this rectangle by using a cutoff on the free-energy. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Berk Hess Sent: Thursday, February 14, 2019 5:41 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] AWH with two bias potentials I see now

Re: [gmx-users] AWH with two bias potentials

on the free-energy. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Berk Hess Sent: Thursday, February 14, 2019 5:41 PM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] AWH with two bias potentials I see now that you used awh-nbias=2 with awh-ndim

Re: [gmx-users] AWH with two bias potentials

From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Cédric Leyrat Sent: Thursday, February 14, 2019 4:32 PM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] AWH with two bias potentials Dear Berk, I do get a set of PMF files at different times for each

Re: [gmx-users] AWH with two bias potentials

Dear Berk, I do get a set of PMF files at different times for each reaction coordinate from gmx awh. Each file has two columns (x=coordinate 1, y=PMF or x=coordinate 2, y=PMF). My coding and maths skills are quite limited so if you have a script that can convert these data to a 2D format, I

Re: [gmx-users] AWH with two bias potentials

gmx awh writes out the 2D (or any-D) PMF to xvg files for different times. The 1D nature of xvg files is not convenient for visualization though, so you need to write a script to convert it to you favorite 2D data format. I probably have a script somewhere for some 2D format (python?) if you

[gmx-users] AWH with two bias potentials

Dear Gromacs users, I'm simulating a system composed of a transmembrane receptor interacting with a 30 kDa soluble protein that sits on top of it. The receptor has a ~ 20 residue tail that is supposed to interact with the soluble protein. I'm trying to predict the most stable conformation of