Simulation and Modelling Art (SMArt)

This toolkit is aimed at facilitating setup and analysis of MD simulations, e.g. perturbation free energy calculations.

Installation

Just clone this repository and you are ready to go

Usage

At the moment, the package supports GROMOS and GROMACS file formats

I/O functionality

parsing

from SMArt.md import parse_top, parse_ff
ff_gr = parse_ff(gromos_ifp_file) # by default, format_type = 'gr'
ff_gm = parse_ff (gromacs_ff_itp_file, format_type = 'gm')

top_gr = parse_top(gromos_top_file) # by default, format_type = 'gr'
top_gm = parse_top(gromacs_top_file, format_type = 'gm')

writing

ff_gr.write_ff(output_file)
ff_gm.write_ff(output_file, format_type = 'gm')

top_gr.write_top(output_file)
top_gm.write_top(output_file, format_type = 'gm') # this will produce a single topology file containing FF information
gm_top_kwargs = dict(format_type='gm', flag_if=True, flag_include=True, sep_ff2itp='top_ff.itp', sep_mol2itp=True)
top_gm.write_top(output_file, flag_segment_order=1, flag_defines_first_include=1, **gm_top_kwargs)
# this separates the FF and molecule type information into separate *itp files that are included in the topology

GROMOS <-> GROMACS conversion

use gr2gm() function to converte GROMOS to GROMACS format and gm2gr() other way around

ff_gr.gr2gm()
top_gr.gr2gm()
ff_gr.write_ff(converted_output_file, format_type='gm')
top_gr.write_top(converted_output_file, format_type='gm')

ff_gm.gm2gr()
top_gm.gm2gr()
ff_gm.write_ff(converted_output_file, format_type='gr')
top_gm.write_top(converted_output_file, format_type='gr')

Perturbation topology preparation

Perturbation topology is based on the maximum common substructure search. This example applies for both point mutation, as well as topologies of 2 different small molecules (e.g. ligands)

from SMArt.md import parse_top
from SMArt import alchemy

format_type = 'gr' # or 'gm'
top_wt = parse_top(wt_top_file, format_type=format_type)
top_mut = parse_top(mut_top_file, format_type=format_type)
# GROMACS
mt_wt, mt_mut = top_gm.molecule_types[mol_id_wt], top_gm_mut.molecule_types[mol_id_mut]
sol = alchemy.point_mutation(mt_wt, mt_mut, ff_dumm = top_gm.get_DUM_type)
sol.toptp.write_itp('toptp.itp', flag_generate_excl_pairs = True)
# GROMOS
sol = alchemy.point_mutation(top_wt, top_mut)
sol.toptp.write_top('toptp.top')
sol.toptp.write_ptp('toptp.ptp')

Simulation update (perturbation free energy calculations)

Automated simulation update scheme - choice of lambda points and simulation time

from SMArt.md.ana import pert_FE
from SMArt.md.gromos.io.ana import read_bar_dhdl, read_exTI
from SMArt.md.gromacs.io.ana import read_bar_data, read_xvg_data

bar_data = {}
for f_path in FE_data_files:
    data, sim_l = read_bar_data(f_path) # gromacs
    data, sim_l = read_bar_dhdl(f_path) # gromos
    pert_FE.combine_bar_dhdl(bar_data, data, sim_l)

initial_t_sim = 1. # initial simulation time per lambda point (1 ns)
LPs_times = dict((temp_lp, initial_t_sim) for temp_lp in bar_data)

seg_score_flag, converged_segments, new_LPs_weights, seg_data_dG_err = pert_FE.update_LPs_times(bar_data)
iter_sim_time = 11. # total simulation time per iteration (if scheme II is used - 11 ns in this case)
new_LPs_times = pert_FE.get_LPs_times(new_LPs_weights, LPs_times, iter_sim_time)

More information is provided in doc directory of the package
Additional useful scripts are can be found in scripts directory of the package

License

SMArt is published under the GNU General Public License (GPLv3)

How to cite?

Please use this reference for citation:
D Petrov. Perturbation Free-Energy Toolkit: An Automated Alchemical Topology Builder. J. Chem. Inf. Model. 2021. (DOI)