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Please pull the required files from (https://gitlab.mpcdf.mpg.de/samsstud/nobel-prize-project.git) to use Metadynamics and get_job.
The below command was used in the cluster with pyiron/latest (Pytho…
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What would be the units of free energy in plumed2-2.8.1 version. I choose distance as a CV in WT-MetaD.
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The LangevinMiddleIntegrator provide consistent result up to 4 femtoseconds timestep, and to converge plumed metadynamics simulation could need longer time, I thinking increase the timestep to allow f…
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Hi,
I updated mlptrain and ran through the DA explicit solvent example. Everything was going fine until I got to Julia. Which version of Julia should I be using? I'm currently using 1.6.7.
Prog…
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I have installed BioSimSpace as following:
conda create -n biosimspace -c conda-forge -c michellab biosimspace
When I used your tutorial, I got an error for visualisation and fun-metaD running. So…
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I am trying to use TorchForce to bias a simulation(box-full of waters). The torch model that calculates the CV looks for nearest neighbors of reference water molecule (within cutoff) then calculates p…
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Hello! I am new to CVHD. I encounter some difficult problems, may I ask you for advice? (The attachment is the out.colvars.traj file)
The out.colvars.traj file obtained by lammps running the CVHD …
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### Background
To end it, we need to clarify some issue:
1. how to tell SCF has been trapped in local minima?
2. how to help SCF jump over it?
Any discussion is welcomed.
### Describe the solut…
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When I load the system with truncated octahedral box using
`mols = sr.load("react.inpcrd","react.prmtop")`
and create OpenMM context for futher EMLE simulation with
`mols, engine = sr.qm.emle(mols,…
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Hi,
I've been trying to run QCG calculations for a small organic molecule using CREST 3.0., but I keep encountering the trial MTD convergence error (after the "quantum cluster growth: GROW" part), re…