[gmx-users] pH during free energy calculation

Dear Experts and users, I am running simulation for solvation free energy calculation using thermodynamic integration approach (as mentioned in Justin's tutorial). My system consist of a cation molecule, an anion molecule and bulk of solvent molecules. I want to understand the pH of my system,

Re: [gmx-users] Error while running free energy simulation.

system as my runs are getting failed at production run phase. How will I decide the end point for equilibration? Thanks and regards, Vivek On 11 November 2014 18:03, Justin Lemkul jalem...@vt.edu wrote: On 11/11/14 2:12 AM, vivek sharma wrote: Dear Users, I am trying to replicate the free

[gmx-users] Error while running free energy simulation.

Thanks in advance regards, Vivek Sharma -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http

[gmx-users] Fwd: Running free energy tutorial for ionic molecules

for the error. regards, Vivek -- Forwarded message -- From: vivek sharma viveksharma.i...@gmail.com Date: 10 October 2014 09:01 Subject: Running free energy tutorial for ionic molecules To: Discussion list for GROMACS users gmx-us...@gromacs.org Hi users and experts, I am

[gmx-users] Running free energy tutorial for ionic molecules

Hi users and experts, I am trying to run a free energy tutorial by Dr Lemkul provided at: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/ My system is an ionic pyridinium molecule unlike the methane molecvule used in the tutorial, following are the steps I am

[gmx-users] Running Free enrgy simulation for ionic molecules

Hi all, I want to calculate free energy of solvation for ionic molecules using thermodynamics approach as mentioned by Garrido et al. Is it possible to apply the same protocol to calculate free energy for ionic molecules as applied over alkanes by Garrido et al.? I am looking for