Peter Eastman
Peter Eastman
Thanks. It sounds like it's the same issue then.
I finally managed to track this down. The problem turned out to be somewhere completely different than I was expecting. When compiling kernels, the CUDA and OpenCL platforms define macros...
> What I don't understand is why the MonteCarloFlexibleBarostat does not get the same mean density as the other two barostats on the CPU platform Are you sure it's a...
Thanks! The fix is in #4618.
This doesn't fix the problem with the PDB file. It just silently ignores it. You asked it to add missing residues, but one of the missing residues has an unknown...
See #194 and #195. We had to make it work that way because neither field consistently identifies chains in all files. The presence of duplicate `auth_` and `label_` fields in...
The NonbondedForce is used to implement the Coulomb interaction. The CustomNonbondedForce is used to implement the LJ interaction. All interactions are correctly accounted for. The LJ parameters are stored in...
> (0.0,) (1.0,) (2.0,) (3.0,) (4.0,) (4.0,) (5.0,) (5.0,) (5.0,) (6.0,) (7.0,) (8.0,) (6.0,) ... (6.0,) Those are the types. It shows particle 0 is type 0, particle 1 is...
An exception is not the same as an NBFIX. An exception is between two particular particles. An NBFIX is between all particles of a particular type. Trying to implement an...
That depends what you mean by "support". PDBFixer can build all residues found in the CCD. But if you want to simulate them, you need parameters. Standard force fields like...