openmm-setup

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Issues with running simulation

1

it returns following issue PFA scripts Building system... Traceback (most recent call last): File "/home/debanjan/Desktop/openmm/run_openmm_simulation.py", line 44, in system = forcefield.createSystem(topology, nonbondedMethod=nonbondedMethod, nonbondedCutoff=nonbondedCutoff, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/debanjan/miniconda3/envs/openmm/lib/python3.12/site-packages/openmm/app/forcefield.py", line 1247, in createSystem...

debanjansen48

Adding missing sidechains and cap termini

1

Hello, thanks for the tool. Does it also add side-chains and cap the termini? Many thanks

GattiMh

Can't abort failed simulation

2

I tried running a simulation using a PDB from the RCSB, and got the error message ``` Building system... Process Process-1: Traceback (most recent call last): File "/Users/choderaj/miniconda3/lib/python3.5/multiprocessing/process.py", line 249,...

jchodera

It's going to be a huge pain if you want to do more than one thing and it always defaults to `/Users/choderaj/openmm_simulation`.

jchodera

Prmtop but no inpcrd

2

I don't know how common this is, but I prepared my system in amber and have an inpcrd, but I have equilibrated trajectories from whence I want to simulate (by...

mpharrigan

The script is written with lots of `append`s and python format strings. Maybe consider having the script be a first-class template that is rendered to a python file

mpharrigan