[gmx-users] Gibbs Energy Calculation, Water/Octanol Partioning

[Dallas Warren]

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.warren at 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-bounces at gromacs.org [mailto:gmx-users-
> bounces at 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.warren at monash.edu
> +61 3 9909 9304
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to
> resemble a nail.