akosny / createremddirs

Automatically generate input for running M-REMD simulations (and more) in Amber.

CreateRemdDirs

Automatically generate input for running M-REMD simulations (and more) in Amber.

Build Status

• GitHub Actions:

About CreateRemdDirs

CreateRemdDirs can be used to automatically generate input for running REMD, H-REMD, M-REMD, and MD simulations that will be chained together (split up into several runs). The general idea is to facilitate long simulation runs on e.g. HPC resources. Currently CreateRemdDirs requires NetCDF libraries to perform checks on Amber trajectories/restarts.

Installation

Typically it is enough to run ./configure gnu on most systems. The job check mode requires NetCDF libraries. If you've already got an Amber installation built with NetCDF it will be enough to ./configure --with-netcdf=$AMBERHOME gnu. Alternatively you can ./configure -no-netcdf gnu to build without NetCDF.

Usage

CreateRemdDirs has 3 modes: input Creation, job Submission, job Checking. There are also 3 types of jobs: Runs, Analysis (--analyze), and Archiving (--archive). Analysis is currently very basic and just consists of stripping, imaging, and sorting (if REMD). Archiving currently consists of placing the stripped/sorted trajectories into a TAR/GZIP archive (along with any fully solvated trajectories specified). The default mode is to Create input for Runs. A typical workflow might consist of the following:

• Create run input.
• Submit run job.
• (After run completion) Check run.
• Create analysis/archive input.
• Submit analysis/archive job.

Help is available via the command line flags '-h' or '--help'. Help on options for various input files is available via the command line flag '--full-help'.

Author

-Daniel R. Roe

Disclaimer and Copyright

CreateRemdDirs is Copyright (c) 2021 Daniel R. Roe. The software is provided AS IS with no warranty. CreateRemdDirs is free software and is licensed under the GPL v2 license (see LICENSE for details).

Brief Example for REMD

CreateRemdDirs uses an input file (by default named remd.opts) that describes how a run should be set up. For example, a 2D M-REMD run (temperature + Hamiltonian) might look like so:

DIMENSION   Temperatures.dat
DIMENSION   Hamiltonians.dat
NSTLIM      500
DT          0.002
NUMEXCHG    100
TEMPERATURE 300.0
MDIN_FILE   pme.remd.in
FULLARCHIVE 0

Creating Input

Basic usage is CreateRemdDirs -b <start run #> -e <end run #>. If only one run is desired only -b need be specified. Runs are set up in subdirectories named run.XXX, where XXX is a 3 digit number corresponding to the run number. Input coordinates can be either specified in the remd.opts file or on the command line with -c (path must be relative to inside the run.XXX directories). Each run after the first is automatically set up to continue from the previous run. Run #0 is special in that it will not be set up as a restart (irest = 0).

The MDIN_FILE should contain Amber MD input flags that belong in the &cntrl namelist. The following flags are set from the remd.opts file and/or automatically: imin (always 0), nstlim, dt, irest, ntx, ig, numexchg, temp0, tempi. All other necessary flags should be in MDIN_FILE. For example:

    ntwx = 5000, ioutfm = 1, ntwr = 100000, ntxo = 2, ntpr = 5000,
    iwrap = 1, nscm = 1000, 
    ntc = 2, ntf = 2, ntb = 1, cut = 8.0,
    ntt = 3, gamma_ln = 1, 
    ntp = 0,

Note that it is recommended that trajectory and restart files be written in NetCDF format (ioutfm=1 and ntxo=2 respectively).

Each REMD run directory will contain a groupfile, input files (in an INPUT subdirectory), a run script (RunMD.sh), and a remd.dim file for M-REMD runs. Output will also be into subdirectories, namely INFO for mdinfo files, LOG for log files (PMEMD only), OUTPUT for mdout files, RST for restart files, and TRAJ for trajectory files. An AMD directory will be created for aMD output files.

Dimensions

The DIMENSION files describe what each dimension looks like. CreateRemdDirs currently supports Temperature, Hamiltonian (Topology), and accelerated MD (aMD) dihedral boost. A dimension file has one header line which describes what kind of dimension it is followed by lines describing how the dimension is set up. For example, a Temperature dimension looks like so:

#Temperature
277.00
281.30
285.70
290.20

A Hamiltonian dimension looks like so:

#Hamiltonian
../../AltDFC.01.PagF.TIP3P.ff14SB.parm7
../../AltDFC.02.PagF.TIP3P.ff14SB.parm7

Note that the paths in a Hamiltonian dimension need to be either absolute or relative to the run directories, i.e. if you 'ls' the file from inside a run.XXX directory it will show up.

An aMD dihedral boost dimension looks like so:

#amd_dihedral
0.0 0.0
50.0 112.0000000000

where the first number corresponds to alpha and the second to the threshhold.

Job Submission

CreateRemdDirs can automatically generate and submit run scripts for PBS and SLURM using options defined in an input file (default 'qsub.opts'). An example looks like so:

JOBNAME test
NODES 16
PPN 8
WALLTIME 24:00:00
EMAIL [email protected]
ACCOUNT testaccount
PROGRAM pmemd
QSUB PBS 
MPIRUN mpiexec -n $THREADS
AMBERHOME /home/droe/Amber/GIT/amber
ANALYZE_FILE analyze.opts
ARCHIVE_FILE analyze.opts

System-wide options can be put into '~/default.qsub.opts', which will always be read. At least JOBNAME and PROGRAM must be specified. The type of queuing system can be changed simply by changing QSUB from PBS to SBATCH.

Jobs are submitted via the '--submit' command flag, e.g. CreateRemdDirs -b 0 -e 1 --submit will submit the already-created input for run.000 and run.001. By default each subsequent job depends on the previous job via batch system holds - this behavior can be changed with the DEPEND input variable. Run input creation and job submission can also be accomplished in one step via the '-s' flag, e.g. CreateRemdDirs -b 0 -e 1 -s.

Job Check

This requires CreateRemdDirs to have been compiled with NetCDF and trajectories and restart files are written in NetCDF format (ioutfm=1 and ntxo=2 respectively). Once a job has completed runs can be checked via the '--check' flag, e.g. CreateRemdDirs -b 0 -e 1 --check. This will check to see if the trajectory length matches what is expected based on input from existing output files. If the trajectory is short, restart times are checked to make sure they are the same. Note that by default for speed only the first replica is checked; all replicas can be checked by using the '--checkall' command line flag.