Re: [gmx-users] Free energy calculation: merge the topology of 2 molecules

> *Gesendet:* Donnerstag, 30. Mai 2013 um 20:48 Uhr > *Von:* "Dejun Lin" > *An:* gmx-users@gromacs.org > *Betreff:* [gmx-users] Free energy calculation: merge the topology of 2 > molecules > Hi all, > > I'm trying to set-up a free energy calculation where a

Aw: [gmx-users] Free energy calculation: merge the topology of 2 molecules

tions though.   Stephan   Gesendet: Donnerstag, 30. Mai 2013 um 20:48 Uhr Von: "Dejun Lin" An: gmx-users@gromacs.org Betreff: [gmx-users] Free energy calculation: merge the topology of 2 molecules Hi all, I'm trying to set-up a free energy calculation where a molecule has +2 charge

[gmx-users] Free energy calculation: merge the topology of 2 molecules

Hi all, I'm trying to set-up a free energy calculation where a molecule has +2 charge in it's native state (state A) and no charge in the mutant (state B). Since the molecule has net +2 charge, I have to add counter-ions to neutralize the system in state A. But in order to transform it to state B