Julien Michel

To add to that, we use a number of tools in the group to do free energy estimation. There is analyse_freenrg written by @chryswoods which does TI, FEP, BAR by...

@davidlmobley yes it would be good if we could load our energies easily into another tool to make sure the same decisions are applied to the raw data. Will keep...

Ah yes ok said that way that sounds easy. Sent from my iPhone > On 9 Feb 2017, at 16:59, David L. Mobley wrote: > > @jmichel80 - just to...

A quick update. The issue was that the input pdb actually contains several molecules, so the Sire parser presumably bails out because the connectivity appears incomplete. parmed doesn't care about...

Good point, @SofiaBariami another workaround may be to split the pdb file with TER statements, that may give you a prm7 file that combine.py can read.

I agree this points to a weakness in the current SOMD code, but there is still a general issue around the modularity of the BSS components. I do wonder what...

That sounds like a reasonable workaround (haven't tested in details yet). For preserving information what about an optional yaml type file that can be passed around to help nodes work...

It is also necessary to keep track of the parameters needed to compute the v-site coordinates from the position of other atoms. See e.g. section 22.5 in http://docs.openmm.org/7.0.0/userguide/theory.html ´´´ OutOfPlaneSite:...

I agree option 2 sounds like the way to go and that it’s not easy to support interoperability of virtual sites as it is still a bit the Wild West...

as the water models are rigid it is trivial to convert TIP3P TIP4P -------------------------------------------------------------- Dr. Julien Michel, Senior Lecturer Room 263, School of Chemistry University of Edinburgh David Brewster road...