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Axel Kohlmeyer
2023-01-13 14:51:21 -05:00
parent 50cc866081
commit 882f155d94
2 changed files with 7 additions and 7 deletions
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tools/emacs/README.md
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@ -71,7 +71,7 @@ The MELPA recipe used for this package is simply:
``` emacs-lisp
(lammps-mode :fetcher github :repo "HaoZeke/lammps-mode")
```
## Caveats
* Does not work with Xemacs [See [this comment](https://github.com/lammps/lammps/pull/1022#issuecomment-408871233)]

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tools/replica/README.md
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@ -24,14 +24,14 @@ email: tanmoy dot 7989 at gmail.com
#### Dependencies
[`mpi4py`](https://mpi4py.readthedocs.io/en/stable/)
[`pymbar`](https://pymbar.readthedocs.io/en/master/) (for getting configurational weights)
[`tqdm`](https://github.com/tqdm/tqdm) (for printing pretty progress bars)
[`mpi4py`](https://mpi4py.readthedocs.io/en/stable/)
[`pymbar`](https://pymbar.readthedocs.io/en/master/) (for getting configurational weights)
[`tqdm`](https://github.com/tqdm/tqdm) (for printing pretty progress bars)
[`StringIO`](https://docs.python.org/2/library/stringio.html) (or [`io`](https://docs.python.org/3/library/io.html) if in Python 3.x)
#### Example
###### REMD Simulation specs
###### REMD Simulation specs
Suppose you ran a REMD simulation for the peptide example using the CHARMM forcefield (see lammps/examples/peptide) in Lammps with the following settings:
- number of replicas = 16
@ -45,7 +45,7 @@ Suppose you ran a REMD simulation for the peptide example using the CHARMM force
So, when the dust settles,
- You'll have 16 replica trajectories. For this tool to work, each replica traj must be named: `<prefix>.<n>.lammpstrj[.gz or .bz2]`, where,
- `prefix` = some common prefix for all your trajectories and (say it is called "peptide")`
- `prefix` = some common prefix for all your trajectories and (say it is called "peptide")`
- `n` = replica number (0-15 in this case). Note: trajectories **must be in default LAMMPS format **(so stuff like dcd won't work)
- You will also have a master LAMMPS log file (`logfn`) that contains the swap history of all the replicas
@ -60,7 +60,7 @@ So, when the dust settles,
- Configurational log-weight calculation (using [`pymbar`](https://github.com/choderalab/pymbar)). Here, this is limited to the canonical (NVT) ensemble **and without biasing restraints** in your simulation. To do this you'd need to have a file (say called `ene.dat`) that stores a 2D (K X N) array of total potential energies, where,
- K = total number of replicas = 16, and N = total number of frames in each replica trajectory (= 1000 / 20 = 50 in this case)
- K = total number of replicas = 16, and N = total number of frames in each replica trajectory (= 1000 / 20 = 50 in this case)
- `ene[k,n]` = energy from n-th frame of k-th replica.