Hannes Loeffler

I'm not sure if I really understand the problem here. Ultimately there is a variable number of free energy/lambda data and as fas as I can see the current Gromacs...

Yes, this is because sander cannot sample the end points. I could probably change the code such that BAR/MBAR free energies are calculated for the existing lambdas only (I assume...

Hi Dan, I'm not sure what exactly the problem is. When I run your command with your data I get the output just fine. Only "issue" is that the tool...

Python 2.7.9 and pymbar 3.0.0 On 20 April 2017 at 22:26, danmermelstein wrote: > Hi @halx , > > Thanks for looking into this! What version of python and pymbar...

This is really an annoying implementation issue with sander. It does not allow you to set lambda < 0.005 or > 0.995. @danmermelstein can probably add more information. It is...

Thanks for the comment. I can provide more info and also data this week.

I have uploaded the data for a simulation mutating ethane to methanol in water (see link below). The transformation has been split into charge only contributions and vdW+bonded contributions. The...

Yes, in stages as you say. So, charges only. Yes, ifsc=1 is required to make use of softcore potentials but they also require scmask for thedefinition of the dummy atoms....

No dummy atoms for the charge only transformation. So here we really transform between the same molecule (same vdW and same bonded parameters) but with the charges of the respective...

One practical thought on this. I think the code should have an understanding of what the various analysis methods "mean". Not sure if there's something in place but e,g, all_methods...