[gmx-users] Thole Potential

Hi, I am trying to use Thole potential to implement polarization effects with drudes. I know NAMD and CHARMM have clear protocols, but I am unable to find much information on how it is implemented in Gromacs. Can someone tell me where I can find an example file to understand the use of [polarizati

Re: [gmx-users] (no subject)

Oh, thanks! On Thu, Oct 6, 2011 at 7:59 PM, Justin A. Lemkul wrote: > > > Sai Janani Ganesan wrote: > >> Hi, >> >> Thanks for the reply! >> >> I tried the rates, and only the terminal with positive rate gets pulled. >> >> The first and the

Re: [gmx-users] (no subject)

pull_vec2. Am I missing anything? Thanks, Sai On Thu, Oct 6, 2011 at 9:14 AM, Justin A. Lemkul wrote: > > > Sai Janani Ganesan wrote: > >> Hi, >> >> I am trying to pull the first from the last amino acid of a protein to >> completely unfold the protein in the X

[gmx-users] (no subject)

Hi, I am trying to pull the first from the last amino acid of a protein to completely unfold the protein in the X direction. I chose the middle amino acid as the reference, and the groups get pulled in the same direction or opposite direction (which is what I want) depending on the trial. I am try