[gmx-users] Gibbs Energy Calculation and charges

2013-11-01 Thread Christopher Neale
Dear Dallas: Seems like you could test Michael's idea by removing all 1-4 NB interactions from your topology. It won't produce any biologically useful results, but might be a worthwhile check to see if indeed this is the issue. To do this, I figure you would set gen-pairs to "no" in the [ defau

[gmx-users] Gibbs Energy Calculation and charges

2013-10-16 Thread Christopher Neale
Ah, I see. I guess that you are using couple-intramol = no (the default in v4.6.3 at least). That means that the intramolecular charge-charge interactions are always at full-strength (and therefore different). I would expect that normal at lambda=0 should be the same as double at lambda=0.5 onl

[gmx-users] Gibbs Energy Calculation and charges

2013-10-16 Thread Christopher Neale
cs.org [mailto:gmx-users- > bounces at gromacs.org] On Behalf Of Dallas Warren > Sent: Thursday, 17 October 2013 9:06 AM > To: Discussion list for GROMACS users > Subject: [gmx-users] Gibbs Energy Calculation and charges > > We have a molecule, and have run two sets of Gibbs energy c

[gmx-users] Gibbs Energy Calculation and charges

2013-10-16 Thread Dallas Warren
We have a molecule, and have run two sets of Gibbs energy calculation, making the charge disappear. One molecule has the normal charges, the other all the charges are doubled. Taking the dHdl results for both and plotting against the charge of a selected atom (charge based at each lambda value)