Shuming Liu

Cannot serialize large system, meet "TypeError: write() argument must be str, not SwigPyObject"

15

So we are using an in-house forcefield and building a simulation system. Since the system is large, we aim to save it as xml file so we can easily load...

Bug with mdtraj.rmsd when computing RMSD of a specific trajectory

5

Hi, So I found a bug with mdtraj.rmsd that when it is computing RMSD of a specific trajectory with a frame of itself, the coordinates saved in the trajectory will...

Encode long-range Coulomb interaction with distance-dependent dielectric into openmm

7

Hi, I want to encode such a Coulomb potential into openmm: $U=\frac{q_i q_j}{4 \pi \epsilon_0 (41.6+41.6\tanh((r-\mu)/\sigma)) r_{ij}}$. So this potential is a Coulomb potential with a distance-dependent dielectric. After some...

May I ask how to draw a specific plane in mol*viewer? For example, I want to draw the plane z=200 in an orthogonal box. I did not find any related...

So how to show a coarse-grained model, such as a protein includes only CA atoms? I can render an all-atom structure, but cannot render CA structures.

openmm plumed write output to bck.0.COLVARS instead of COLVARS

10

Hi, I found when I simulate a specific system with openmm plumed on GPU by CUDA, the plumed output, which should be written to COLVARS, is actually written to bck.0.COLVARS...