<<<<<<< HEAD Reweighting-CPMD-TASS
Temperature Accelerated Sliced Sampling (TASS) method combines the temperature accelerated molecular dynamics with umbrella sampling and
metadynamics to sample the collective variable space in an efficient manner.
[Ref :
Exploring high dimensional free energy landscapes: Temperature accelerated sliced sampling J. Chem. Phys. 146, 094108 (2017).
[![DOI] https://doi.org/10.1063/1.4977704
Awasthi, S, Nair, NN. Exploring high‐dimensional free energy landscapes of chemical reactions. WIREs Comput Mol Sci. 2019.
[![DOI] https://doi.org/10.1002/wcms.1398 ]
This Modular Fortran program unbias the Probability of TASS output generated in CPMD/PLUMED run, which can be used to compute multidimensional (1D/2D) free energy via WHAM reweighting. It can also directly generate 1D free energy using Mean Force method (MF).
1D and 2D Basis Spline interpolation can be performed to find intermediate points in free energy .
+ UPDATE :: "Reweight Biased Simulation from both CPMD and PLUMED Packages."
+ IMPORTANT :: ALL THE ARGUMENTS IN THE RUN FILE ARE CASE SENSITIVE.
+ COLVAR file must have the format of CV1_ext CV2_ext CV3_ext ....
- !! PERIODICITY IS NOT YET IMPLIMENTED !![Ref : https://github.com/jacobwilliams/bspline-fortran]
#---------------------------------------------------------------------------------------------------------------------------------------------
```bash
#!/bin/bash
bin/Probability_analysis.x # executable
-T0 300 # Physical system Temperature
-T 1000 # CV Temperature
-prog_name CPMD/PLUMED # Name of MD package (CPMD/PLUMED)
-bias_fact 1500 # Metadynamics Bias Factor
-tmin 5000 # Minimum MD steps to compute Probability
-ncv 5 # Total CV's in TASS Simulation
-UCV 1 # Umbrella CV index
-MTD n # y/n IF Metadynamics performed durung simulation
-MCV 0 # IF MTD=y then Metadynamics CV index [else=0]
-tool pmf # pmf/probT [pmf-->compute potential of mean force ; probT --> Unbias Probability]
-interpolate # Basis Spline 1D interpolation if one wants to do for pmf free energy
-nr 14 # Number of replica (total umbrella window during simulation)
-Prob_nD 1 # Dimension of Probabilty to be generated [1/2/3]
-CV_num 1 2 # Probabilty generated along CV indicis [1 --> 1D ; 1 2 --> for 2D along CV1 and CV2 etc..]
-pfrqMD 1 # Frequency of update in cvmdck_mtd file during run
-dtMTD 200 # Frequency of Hill Update during Metadynamics
-grid 1.5 4.5 0.02 1.0 10.0 0.02 1.0 9.0 0.02 3.0 5.0 0.02 1.0 6.0 0.05 ,\ # gridmin gridmax griddif for every CV
INSTALL :
./configure
#Choose compier [gnu/intel]
./configure -h # for more options
A Makefile will be created
...
make install : create executabls
make bspline : compile B-spline modules
make clean : remove object and mod files
make distclean : clean the directoryHow to Run -->
"-------------"
A bash script is given along with the program (run_tass.sh)
Create execute permission by following command :
chomd 755 run_tass.sh
To compute Free Energy using Mean Force method =-> -tool pmf (case sensitive)
To compute multidimensional probabilities =-> -tool probT (case sensitive)RAHUL VERMA
DEPARTMENT OF CHEMISTRY
IIT KANPUR, INDIA
Email : [email protected]
Reweight TASS based biased simulation from CPMD and PLUMED
f4e6ceb5021c9e199a36eb6bdf4e33d9d271caf4
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