Re: [gmx-users] Inconsistent behavior for bonds involving dummy atoms for alchemical perturbation

2016-03-20 Thread Justin Lemkul
On 3/17/16 6:04 PM, Ryan Muraglia wrote: Dear GROMACS users, I've been attempting to calculate delta G values for GXG tripeptide mutations as a test case to validate and benchmark my set up, but I have run into a host of issues and curiosities, one of which I describe below. Depending on the

[gmx-users] Inconsistent behavior for bonds involving dummy atoms for alchemical perturbation

2016-03-18 Thread Ryan Muraglia
Dear GROMACS users, I've been attempting to calculate delta G values for GXG tripeptide mutations as a test case to validate and benchmark my set up, but I have run into a host of issues and curiosities, one of which I describe below. Depending on the direction in which I carry out a mutation, a