Re: [gmx-users] energy comparison

2012-10-02 Thread Justin Lemkul
On 10/2/12 2:45 PM, Edward Deira wrote: not that off-base, actually. one of my aims is to compare two different proteins with the same ligand and try to figure out which system is energetically more favourable without having to go through qm/mm. so i suppose the proper way would be estimating t

Re: [gmx-users] energy comparison

2012-10-02 Thread Edward Deira
not that off-base, actually. one of my aims is to compare two different proteins with the same ligand and try to figure out which system is energetically more favourable without having to go through qm/mm. so i suppose the proper way would be estimating the "absolute" free energy of the system. ca

Re: [gmx-users] energy comparison

2012-10-02 Thread Justin Lemkul
On 10/2/12 12:49 PM, Edward Deira wrote: Dear all, From the computational side of the question, can one compare the final energy values at the end of a simulation ? Are those energy values are meaningful ? Can I, with proper chemical judgement, say that a lower (more negative) value will cor