-
I am writing a program to resume metadynamics (MTD) in openmm-plumed after it has been interrupted. I am facing a problem where the potential immediately after resumption does not reproduce the potent…
-
@MoleOrbitalHybridAnalyst
你好,请问怎么使用pyemma处理metadynamics轨迹?
参考了你的[tram2d.py](https://github.com/MoleOrbitalHybridAnalyst/mdtools/blob/master/tram2d.py),但是没怎么看懂,能给点说明?
filenames[thermo_index]是什么…
-
This is a thread to discuss the creation of a tutorial showing how to implement funnel metadynamics within BioSimSpace.
-
Hi,
I am trying to use OpenMM to run a metadynamics simulation, in which i would like to get the free energy during the dissemble of alpha-helix to random coil. Here is the code and error. Could yo…
-
Currently the `Metadynamics` method only supports static number of gaussians ([code](https://github.com/SSAGESLabs/PySAGES/blob/b1f9da9d1521d0c87b6592732a50bfbc9c947368/pysages/methods/metad.py#L171))…
-
Hi, I'm using the OpenMM metadynamics implementation and I would like to make a suggestion: having an option of keeping the previous bias files, instead of having them overwritten. This is really usef…
-
I'm testing out the metadynamics walkers implementation and I'm seeing odd behaviour. When walker simulations are running simultaneously, the deposited biases are huge, in the order of 10^6 kJ/mol, ev…
-
I am interested in kerseq2hills.py. Kindly guide how to execute the script.
unable to add Desmond scripts using maestro. How to execute them?
-
I put the system with 85 atoms ,322 electrons on NCI mode conformational search with the following Slurm job script.
#!/bin/sh
#SBATCH --job-name=bbphenol
#SBATCH --account=Chemistry
#SBATCH --nod…
-
I am running an AIMD Metadynamics calculation using cp2k for a small system (89 atoms and 256 electrons). I also have PLUMED patched for enabling Metadynamics calculations. The calculations would run …