Skip to main content

PypKa + GROMACS = an awesome Constant-pH Molecular Dynamics implementation

Project description

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

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

pypkamd-0.4.0.tar.gz (737.3 kB view hashes)

Uploaded source

Built Distribution

pypkamd-0.4.0-py3-none-any.whl (801.9 kB view hashes)

Uploaded py3

Supported by

AWS AWS Cloud computing Datadog Datadog Monitoring Facebook / Instagram Facebook / Instagram PSF Sponsor Fastly Fastly CDN Google Google Object Storage and Download Analytics Huawei Huawei PSF Sponsor Microsoft Microsoft PSF Sponsor NVIDIA NVIDIA PSF Sponsor Pingdom Pingdom Monitoring Salesforce Salesforce PSF Sponsor Sentry Sentry Error logging StatusPage StatusPage Status page