FYI, the sd versus md is stable and our runs are now completing fully and we are obtaining the correct Gibbs energy values.
Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 dallas.war...@monash.edu +61 3 9909 9304 --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. > -----Original Message----- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users- > boun...@gromacs.org] On Behalf Of Dallas Warren > Sent: Wednesday, 8 September 2010 3:41 PM > To: Discussion list for GROMACS users > Subject: RE: [gmx-users] Gibbs Energy Calculation, Water/Octanol > Partioning > > Justin, > > > Have you tried using the sd integrator? That's what the authors of > this paper > > used. I don't know if there are stability issues with md vs. sd, but > it's a > > starting point. > > That does appear to be the issue. We have repeated the pentane in > octanol lambda runs and it completed without any errors. Going back > now to repeat a few other things, and will report back once have > checked everything out. > > Catch ya, > > Dr. Dallas Warren > Medicinal Chemistry and Drug Action > Monash Institute of Pharmaceutical Sciences, Monash University > 381 Royal Parade, Parkville VIC 3010 > dallas.war...@monash.edu > +61 3 9909 9304 > --------------------------------- > When the only tool you own is a hammer, every problem begins to > resemble a nail.
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