Reweighing-TASS-1.2

Brief Description

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 ] Pal, A., Pal, S., Verma, S., Shiga, M., Nair, N. N., Mean force based temperature accelerated sliced sampling: Efficient reconstruction of high dimensional free energy landscapes. [![https://doi.org/10.1002/jcc.26727] ]

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. Alos, it can also compute 1D and 2D free enrgy using Mean Force method (PMF).

Basis Spline interpolation can be performed to find intermediate points in free energy.

UPDATE :: "1D and 2D free energy will be computed with Mean Force" IMPORTANT :: "Input variables in the file are case sensitive (i.e. +-> can be turn on/off with upper/lower case.)" [Ref : https://github.com/jacobwilliams/bspline-fortran]

This is an updated version of version 1.1, as this can now read input arguments from an input file insted of terminal.

Modular Code Written by:- Rahul Verma

#---------------------------------------------------------------------------------------------------------------------------------------------

NUMBER OF CV		 	# Total CV's Chosen in the Simulation	
5
CODE NAME			# Name of MD the Package (CPMD/PLUMED)
CPMD
NUMBER OF UMBRELLA		# Number of replica (total umbrella window during simulation)
22
UCV COLUMN			# Umbrella CV Index
1
MTD ENABLED			# IF Metadynamics performed durung simulation (y/n)
n
MTD CV COLUMN			# IF MTD ENABLED then Metadynamics CV Index [else=0]
2
MTD BIAS FACTOR			# Metadynamics Bias Factor
1200
SYSTEM TEMP			# Physical system Temperature
300
CV TEMP				# CV Temperature
1000
TMIN				# Minimum MD steps to Compute Probability
1000
TMAX				# Maximum MD steps to Compute Probability
14000
REWEIGHTING TOOL		# pmf/prob [pmf-->compute potential of mean force ; prob --> Unbias Probability]
pmf
PROBABILITY DIMENSION		# Dimension of Probability/Free Energy(MeanForce) to be generated [1/2]
2
PROBABILITY CV INDEX		# Probability/Free Energy(MeanForce) generated along CV indicis [1 --> 1D ; 1 2 --> 2D along CV1 and CV2 etc..]
1 3
STATISTICAL ERRORS BLOCK SIZE   # Compute Statistical Error in Block Data [optimal Block Size --> 4/5]
4
CV PRINT FREQUENCY		# Frequency of update in cvmdck_mtd file during run
1
MTD PRINT FREQUENCY		# Frequency of Hill Update during Metadynamics
10
GRIDS				# gridmin gridmax griddif for every CV [NCV]
1.8 6.0  0.01
0.5 5.0  0.05
1.0 8.0  0.01
1.0 10.0 0.01
1.0 8.0  0.01

```Makefile
INSTALL :
Modify Makefile to change the compiler [if needed]
Type...
make install   : create executabls
make bspline   : compile B-spline modules
make clean     : remove object and mod files
make distclean : clean the directory

How to Run -->
"-------------"
A bash script is given along with the program (run.sh) 
Create execute permission by following command :
chmod 755 run.sh
./run.sh

Or it can be run directly from the command line as:
----------------------------------------------------
$path_to_install_folder/bin/tass_analysis.x < input.tass   # input file name

UPDATE:: Version 1.3 will be updated soon with more features and some hands-on examples.

AUTHOUR

RAHUL VERMA
DEPARTMENT OF CHEMISTRY
IIT KANPUR, INDIA
Email : vrahul@iitk.ac.in