PypKa-MD
PypKa + MD = constant-pH molecular dynamics
Implementation of the stochastic titration method 1
[1] Baptista et al., J. Chem. Phys. 117, 4184 (2002) DOI: 10.1063/1.1497164
Installation
python3 -m pip install pypkamd
Dependencies
Both PypKa and GROMACS are required to be installed in the system.
- PypKa >= 2.7.1
- GROMACS >=5.1.5
When running in pKAI-MD mode there are extra dependencies:
- pege >= 1.1.1
- torch_geometric >= 2.0.0
Please refer to the installation guide of torch geometric to install the proper version in accordance to your CUDA and OS.
python3 -m pip install pege
# EXAMPLE FOR CUDA10.2
# python3 -m pip install torch-scatter torch-sparse torch-cluster torch-spline-conv torch-geometric -f https://data.pyg.org/whl/torch-1.10.0+cu102.html
Usage
Upon installation a PypKa-MD executable should have been added to your bin. You may call it directly giving as an argument a modified GROMACS .mdp input file to include Constant-pH specific variables.
pypkamd System.mdp
In case the executable as not been added to your bin, you may use:
python3 -m pypkamd System.mdp
You may find an example .mdp file in /utils/cphmd.mdp.
; GROin = system_000.gro ; input GRO file
; TOPin = system_000.top ; input TOP file
; DATin = fixgro.dat ; input DAT file (to be removed)
; NDXin = system.ndx ; input NDX file
; sysname = system_001 ; output files root name
; sites = all ; to be titrating sites in the protein
; titrating_group = Protein ; index group of the protein
; nCycles = 50 ; number of CpHMD cycles
;; total simulation time = nCycles * tau_prot
;; 1ns = 50 * 20ps
; nCPUs = 4 ; number of CPUs to be used
; pH = 7.0 ; pH value of the protonation states sampling
; ionicstr = 0.1 ; ionic strength used in PB
; GroDIR="/gromacs/gromacs-5.1.5_pH_I/bin/" ; GROMACS bin path
