mxmd Command Help
Command: $SCHRODINGER/mxmd
usage:
Mixed Solvent Molecular Dynamics (MxMD) is a hotspot mapping technique that relies on
molecular simulations of proteins in binary solvent mixtures. These mixtures consist of
water and small organic cosolvent probes that mimic binding counterpart of your protein.
Application of MxMD has been effective in the identification and characterization
of binding sites or protein-protein interfaces (PPI) along a protein surface.
* Run a new job:
$SCHRODINGER/mxmd -probe acetone,acetonitrile,imidazole -time 5000.0 -HOST <main-host> -SUBHOST <subhost> -JOBNAME <jobname> -nsim_per_probe 10 input.mae
positional arguments:
inp_file A Maestro structure file
options:
-h, --help show this help message and exit
-ff {OPLS4|OPLS5} Specify the forcefield to use. Default: OPLS4.
-prepare Do not run job. Only prepare multisim input files.
-JOBNAME <string> Specify the job name.
-maxjob <integer> Maximum number of simultaneous subjobs. Default: 0
(unlimited)
-energy-groups Compute energy groups during production simulations.
-enable-metal-force-field
Enable metal support for the OPLS5 force field.
-time <real> Specify time (in ps) for the production simulation
stage. Default: 5000.0.
-time-equilibrate <real>
Specify time (in ps) for the equilibration simulation
stage. Default: 15000.0
-probe <string> Specify the cosolvent probes. Default:
acetonitrile,isopropanol,pyrimidine; Supported probes:
1-3-oxazinan-2-one, 1-isoquinolinone,
1-methyl-1h-indazole, 1-naphthol, 1h-indazole,
2-cyanophenol, 2-isoquinolinone, 2-methyl-2h-indazole,
2-naphthol, 2h-indazole, 3-cyanophenol, 4-cyanophenol,
acetaldehyde, acetamide, aceticacid, acetone,
acetonitrile, androstenol, benzene, benzothiazole,
cyanobenzene, diethylamine, dimethylsulfoxide,
ethanol, formamide, furan, glycerol, imidazole,
isatin, isobutane, isonicotinonitrile, isopropanol,
isopropylamine, isoquinoline, methylamine,
methylsulfonylmethane, morpholine, naphthol,
nicotinonitrile, nmethylacetamide, oxane, oxazole,
oxirane, oxiranemethanol, phenol, picolinonitrile,
piperidine, propyne, pyrazine, pyridazine, pyridine,
pyrimidine, quinoline, resorcinol, sulfamide,
thiazole, triethylamine, trifluoroethanol, urea. For
use of custom probe(s), additionally provide the
-custom-dir option
-membrane MEMBRANE Build membrane-containing system, use membrane-
specific MD protocol to run subjobs. Available
membrane bilayers are: POPE, DMPC, DPPC, POPC.
Default: None
-init-water-buffer <real>
Specify a guess for the initial water box buffer. The
box will then be shrunk to match volume/volume ratio
Default: 17.0
-nsim-per-probe <integer>, -nsim_per_probe <integer>
Specify number of simulations per probe Default: 10
-custom-probe-dir CUSTOM_PROBE_DIR
Specify custom probe directory. There must be a
<probe_name>.box.mae file in this directory for each
custom probe passed in using -custom-probe-
dir.Default: No custom probe directory
-sitemap-cpu-host SITEMAP_CPU_HOST
Specify CPU host for SiteMap analysis, in the format
HOST:MAX_SITEMAP_JOBS. If provided, SiteMap will be
run on protein structures after MxMD cleanup. Default:
No SiteMap analysis
Job Control Options:
-HOST <hostname> Run job remotely on the indicated host entry.
-WAIT Do not return a prompt until the job completes.
-LOCAL Do not use a temporary directory for job files. Keep
files in the current directory.
-D, -DEBUG Show details of Job Control operation.
-TMPDIR TMPDIR The name of the directory used to store files
temporarily during a job.
-SAVE Return zip archive of job directory at job completion.
-OPLSDIR OPLSDIR Specifies directory for custom forcefield parameters.
Standard Options:
-SUBHOST <hostname> or -SUBHOST <hostname:nproc> or -SUBHOST "hostname1:nproc1 ... hostnameN:nprocN"
Run the subjobs on the specified hosts. The driver is
run on the host specified with -HOST.
-RETRIES RETRIES If a subjob fails for any reason, it will be retried
RETRIES times.
-RESTART Restart a previously failed job, utilizing any already
completed subjobs.