Commit 7fd449a0 authored by Berk Onat's avatar Berk Onat

Initial commit for NAMD parser

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# NAMD Parser
[NOMAD Laboratory CoE](http://nomad-coe.eu) parser for [NAMD](http://www.ks.uiuc.edu/Research/namd/)
## Version 0.0.1
This is the parser for NAMD Molecular Dynamics (namd2) in [NAMD](http://www.ks.uiuc.edu/Research/namd/).
The official version lives at:
git@gitlab.mpcdf.mpg.de:nomad-lab/parser-namd.git
You can browse it at:
https://gitlab.rzg.mpg.de/nomad-lab/parser-namd
It relies on having the nomad-meta-info and the python-common repositories one level higher.
The simplest way to have this is to check out nomad-lab-base recursively:
git clone --recursive git@gitlab.mpcdf.mpg.de:nomad-lab/nomad-lab-base.git
This parser will be in the directory parsers/namd of this repository.
## Running and Testing the Parser
### Requirements
The required python packages can be installed with (see [python-common](https://gitlab.rzg.mpg.de/nomad-lab/python-common)):
pip install -r nomad-lab-base/python-common/requirements.txt
### Usage
NAMD md (namd2 executable) log output files can be parsed with:
python NAMDParser.py [path/toFile]
### Test Files
Example log output files of NAMD can be found in the directory test/examples.
More details about the calculations and files will be explained in this README file.
<?xml version="1.0" encoding="UTF-8"?>
<project version="4">
<component name="ProjectRootManager" version="2" project-jdk-name="Python 3.6.1 virtualenv at /labEnv3" project-jdk-type="Python SDK" />
</project>
\ No newline at end of file
<?xml version="1.0" encoding="UTF-8"?>
<project version="4">
<component name="ProjectModuleManager">
<modules>
<module fileurl="file://$PROJECT_DIR$/.idea/parser-amber.iml" filepath="$PROJECT_DIR$/.idea/parser-amber.iml" />
</modules>
</component>
</project>
\ No newline at end of file
<?xml version="1.0" encoding="UTF-8"?>
<module type="PYTHON_MODULE" version="4">
<component name="NewModuleRootManager">
<content url="file://$MODULE_DIR$" />
<orderEntry type="inheritedJdk" />
<orderEntry type="sourceFolder" forTests="false" />
</component>
<component name="TestRunnerService">
<option name="projectConfiguration" value="Nosetests" />
<option name="PROJECT_TEST_RUNNER" value="Nosetests" />
</component>
</module>
\ No newline at end of file
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import logging
import os
PARSERNAME = "NAMD"
PROGRAMNAME = "namd"
PARSERVERSION = "0.0.1"
PARSERMETANAME = PARSERNAME.lower()
PARSERTAG = 'x_' + PARSERMETANAME
PARSER_INFO_DEFAULT = {
'name' : PARSERMETANAME+'-parser',
'version': PARSERVERSION
}
META_INFO_PATH = os.path.normpath(os.path.join(
os.path.dirname(os.path.abspath(__file__)),
"../../../../nomad-meta-info/meta_info/nomad_meta_info/"+PARSERMETANAME+".nomadmetainfo.json"))
LOGGER = logging.getLogger("nomad."+PROGRAMNAME+"Parser")
def set_excludeList(self):
"""Sets the exclude list for x_
Returns:
the list of names
"""
excludelist = [
PARSERTAG+'_mdin_verbatim_writeout',
PARSERTAG+'_dumm_text',
PARSERTAG+'_dummy',
PARSERTAG+'_mdin_wt'
]
excludelist.extend([PARSERTAG+'_mdin_file_%s' % fileNL.lower() for fileNL in self.fileDict.keys()])
excludelist.extend([PARSERTAG+'_mdin_%s' % cntrlNL.lower() for cntrlNL in self.cntrlDict.keys()])
excludelist.extend([PARSERTAG+'_mdin_%s' % ewaldNL.lower() for ewaldNL in self.ewaldDict.keys()])
excludelist.extend([PARSERTAG+'_mdin_%s' % qmmmNL.lower() for qmmmNL in self.qmmmDict.keys()])
return excludelist
def set_includeList():
"""Sets the include list for x_
Returns:
the list of names
"""
includelist = []
return includelist
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import sys
import os
import os.path
basedir = os.path.dirname(os.path.abspath(__file__))
commondir = os.path.normpath(os.path.join(basedir,"../../../../python-common/common/python"))
if not commondir in sys.path:
sys.path.insert(0, commondir)
package eu.nomad_lab.parsers
import eu.nomad_lab
import eu.nomad_lab.DefaultPythonInterpreter
import org.{ json4s => jn }
import eu.{ nomad_lab => lab }
import scala.collection.breakOut
object NAMDParser extends SimpleExternalParserGenerator(
name = "NAMDParser",
parserInfo = jn.JObject(
("name" -> jn.JString("NAMDParser")) ::
("parserId" -> jn.JString("NAMDParser" + lab.NAMDVersionInfo.version)) ::
("versionInfo" -> jn.JObject(
("nomadCoreVersion" -> jn.JObject(lab.NomadCoreVersionInfo.toMap.map {
case (k, v) => k -> jn.JString(v.toString)
}(breakOut): List[(String, jn.JString)])) ::
(lab.NAMDVersionInfo.toMap.map {
case (key, value) =>
(key -> jn.JString(value.toString))
}(breakOut): List[(String, jn.JString)])
)) :: Nil
),
mainFileTypes = Seq("text/.*"),
mainFileRe = """\s*Info:\s*NAMD\s*[0-9.]+\s*for\s*""".r,
cmd = Seq(DefaultPythonInterpreter.pythonExe(), "${envDir}/parsers/gromacs/parser/parser-namd/NAMDParser.py",
"${mainFilePath}"),
resList = Seq(
"parser-namd/NAMDParser.py",
"parser-namd/NAMDDictionary.py",
"parser-namd/NAMDCommon.py",
"parser-namd/setup_paths.py",
"nomad_meta_info/public.nomadmetainfo.json",
"nomad_meta_info/common.nomadmetainfo.json",
"nomad_meta_info/meta_types.nomadmetainfo.json",
"nomad_meta_info/namd.nomadmetainfo.json"
) ++ DefaultPythonInterpreter.commonFiles(),
dirMap = Map(
"parser-namd" -> "parsers/namd/parser/parser-namd",
"nomad_meta_info" -> "nomad-meta-info/meta_info/nomad_meta_info",
"python" -> "python-common/common/python/nomadcore"
) ++ DefaultPythonInterpreter.commonDirMapping(),
metaInfoEnv = Some(lab.meta.KnownMetaInfoEnvs.gromacs)
)
package eu.nomad_lab.parsers
import org.specs2.mutable.Specification
object NAMDParserTests extends Specification {
"NAMDParserTest" >> {
"[tiny with 507 atoms] test with json-events" >> {
ParserRun.parse(NAMDParser, "parsers/gromacs/test/examples/tiny/tiny.log", "json-events") must_== ParseResult.ParseSuccess
}
"[tiny with 507 atoms] test with json" >> {
ParserRun.parse(NAMDParser, "parsers/gromacs/test/examples/tiny/tiny.log", "json") must_== ParseResult.ParseSuccess
}
"[apoa1-trajectory with 92224 atoms] test with json-events" >> {
ParserRun.parse(NAMDParser, "parsers/gromacs/test/examples/apoa1-trajectory/apoa1.log", "json-events") must_== ParseResult.ParseSuccess
}
"[apoa1-trajectory with 92224 atoms] test with json" >> {
ParserRun.parse(NAMDParser, "parsers/gromacs/test/examples/apoa1-trajectory/apoa1.log", "json") must_== ParseResult.ParseSuccess
}
}
}
# Tests:
### Source of Tests:
The tests are taken from NAMD (version 2.12) examples in [NAMD](http://www.ks.uiuc.edu/Research/namd/utilities/).
### Example Tests:
#### ApoA1 benchmark
92224 atoms, periodic, PME [NAMD home link](http://www.ks.uiuc.edu/Research/namd/utilities/apoa1/)
#### tiny benchmark
507 atoms, periodic, PME [NAMD home link](http://www.ks.uiuc.edu/Research/namd/utilities/tiny/)
#### Interactive BPTI benchmark
882 atoms, small [NAMD home link](http://www.ks.uiuc.edu/Research/namd/utilities/bpti_imd/)
#### ER-GRE benchmark
36573 atoms, spherical [NAMD home link](http://www.ks.uiuc.edu/Research/namd/utilities/er-gre/)
(FFTW-2.1.3 (108 537 1 0 123 1 1 209 0) (36 537 1 0 123 1 1 77 0) (12 537 1 0 123 1 0 276 0) (4 537 1 0 123 1 0 100 0) (54 537 1 0 123 1 1 143 0) (18 537 1 0 123 1 1 77 0) (6 537 1 0 123 1 0 144 0) (2 537 1 0 123 1 0 56 0) (27 537 1 0 123 1 1 77 0) (9 537 1 0 123 1 0 210 0) (3 537 1 0 123 1 0 78 0) (108 537 1 0 287 1 1 209 0) (36 537 1 0 287 1 1 77 0) (12 537 1 0 287 1 0 276 0) (4 537 1 0 287 1 0 100 0) (54 537 1 0 287 1 1 209 0) (18 537 1 0 287 1 1 77 0) (6 537 1 0 287 1 0 144 0) (2 537 1 0 287 1 0 56 0) (27 537 1 0 287 1 1 77 0) (9 537 1 0 287 1 0 210 0) (3 537 1 0 287 1 0 78 0) (108 537 -1 0 123 1 1 198 0) (36 537 -1 0 123 1 1 66 0) (12 537 -1 0 123 1 0 265 0) (4 537 -1 0 123 1 0 89 0) (54 537 -1 0 123 1 1 198 0) (18 537 -1 0 123 1 1 66 0) (6 537 -1 0 123 1 0 133 0) (2 537 -1 0 123 1 0 45 0) (27 537 -1 0 123 1 1 66 0) (9 537 -1 0 123 1 0 199 0) (3 537 -1 0 123 1 0 67 0) (108 537 -1 0 287 1 1 198 0) (36 537 -1 0 287 1 1 66 0) (12 537 -1 0 287 1 0 265 0) (4 537 -1 0 287 1 0 89 0) (54 537 -1 0 287 1 1 198 0) (18 537 -1 0 287 1 1 66 0) (6 537 -1 0 287 1 0 133 0) (2 537 -1 0 287 1 0 45 0) (27 537 -1 0 287 1 1 66 0) (9 537 -1 0 287 1 0 199 0) (3 537 -1 0 287 1 0 67 0) (5 529 -1 1 1 1 4 112 0) (2 529 -1 1 1 1 4 46 0) (10 529 -1 1 1 1 4 222 0) (4 529 -1 1 1 1 4 90 0) (20 529 -1 1 1 1 6 47 0) (8 529 -1 1 1 1 4 178 0) (40 529 -1 1 1 1 6 91 0) (16 529 -1 1 1 1 4 354 0) (80 529 -1 1 1 1 6 113 0) (3 537 -1 0 41 1 0 67 0) (9 537 -1 0 41 1 0 199 0) (27 537 -1 0 41 1 1 66 0) (2 537 -1 0 41 1 0 45 0) (6 537 -1 0 41 1 0 133 0) (18 537 -1 0 41 1 1 66 0) (54 537 -1 0 41 1 1 198 0) (4 537 -1 0 41 1 0 89 0) (12 537 -1 0 41 1 0 265 0) (36 537 -1 0 41 1 1 132 0) (108 537 -1 0 41 1 1 198 0) (3 537 -1 0 1107 1 0 67 0) (9 537 -1 0 1107 1 0 199 0) (27 537 -1 0 1107 1 1 66 0) (2 537 -1 0 1107 1 0 45 0) (6 537 -1 0 1107 1 0 133 0) (18 537 -1 0 1107 1 1 66 0) (54 537 -1 0 1107 1 1 198 0) (4 537 -1 0 1107 1 0 89 0) (12 537 -1 0 1107 1 0 265 0) (36 537 -1 0 1107 1 1 66 0) (108 537 -1 0 1107 1 1 198 0) (3 537 1 0 1107 1 0 78 0) (9 537 1 0 1107 1 0 210 0) (27 537 1 0 1107 1 1 77 0) (2 537 1 0 1107 1 0 56 0) (6 537 1 0 1107 1 0 144 0) (18 537 1 0 1107 1 1 77 0) (54 537 1 0 1107 1 1 209 0) (4 537 1 0 1107 1 0 100 0) (12 537 1 0 1107 1 0 276 0) (36 537 1 0 1107 1 1 77 0) (108 537 1 0 1107 1 1 209 0) (5 529 1 1 1 1 5 125 0) (2 529 1 1 1 1 5 59 0) (10 529 1 1 1 1 5 235 0) (4 529 1 1 1 1 5 103 0) (20 529 1 1 1 1 6 58 0) (8 529 1 1 1 1 5 191 0) (40 529 1 1 1 1 6 102 0) (16 529 1 1 1 1 5 367 0) (80 529 1 1 1 1 6 234 0) (3 537 1 0 41 1 0 78 0) (9 537 1 0 41 1 0 210 0) (27 537 1 0 41 1 1 77 0) (2 537 1 0 41 1 0 56 0) (6 537 1 0 41 1 0 144 0) (18 537 1 0 41 1 1 77 0) (54 537 1 0 41 1 1 209 0) (4 537 1 0 41 1 0 100 0) (12 537 1 0 41 1 0 276 0) (36 537 1 0 41 1 1 77 0) (108 537 1 0 41 1 1 209 0))
\ No newline at end of file
(FFTW-2.1.3 (5 529 -1 1 1 1 4 112 0) (2 529 -1 1 1 1 4 46 0) (10 529 -1 1 1 1 4 222 0) (4 529 -1 1 1 1 4 90 0) (20 529 -1 1 1 1 6 47 0) (8 529 -1 1 1 1 4 178 0) (40 529 -1 1 1 1 6 91 0) (16 529 -1 1 1 1 4 354 0) (80 529 -1 1 1 1 6 179 0) (3 537 -1 0 41 1 0 67 0) (9 537 -1 0 41 1 0 199 0) (27 537 -1 0 41 1 1 66 0) (2 537 -1 0 41 1 0 45 0) (6 537 -1 0 41 1 0 133 0) (18 537 -1 0 41 1 1 66 0) (54 537 -1 0 41 1 1 132 0) (4 537 -1 0 41 1 0 89 0) (12 537 -1 0 41 1 0 265 0) (36 537 -1 0 41 1 1 66 0) (108 537 -1 0 41 1 1 198 0) (3 537 -1 0 4428 1 0 67 0) (9 537 -1 0 4428 1 0 199 0) (27 537 -1 0 4428 1 1 66 0) (2 537 -1 0 4428 1 0 45 0) (6 537 -1 0 4428 1 0 133 0) (18 537 -1 0 4428 1 1 66 0) (54 537 -1 0 4428 1 1 132 0) (4 537 -1 0 4428 1 0 89 0) (12 537 -1 0 4428 1 0 265 0) (36 537 -1 0 4428 1 1 66 0) (108 537 -1 0 4428 1 1 198 0) (3 537 1 0 4428 1 0 78 0) (9 537 1 0 4428 1 0 210 0) (27 537 1 0 4428 1 1 77 0) (2 537 1 0 4428 1 0 56 0) (6 537 1 0 4428 1 0 144 0) (18 537 1 0 4428 1 1 55 0) (54 537 1 0 4428 1 1 143 0) (4 537 1 0 4428 1 0 100 0) (12 537 1 0 4428 1 0 276 0) (36 537 1 0 4428 1 1 77 0) (108 537 1 0 4428 1 1 209 0) (5 529 1 1 1 1 5 125 0) (2 529 1 1 1 1 5 59 0) (10 529 1 1 1 1 5 235 0) (4 529 1 1 1 1 5 103 0) (20 529 1 1 1 1 6 58 0) (8 529 1 1 1 1 5 191 0) (40 529 1 1 1 1 6 102 0) (16 529 1 1 1 1 5 367 0) (80 529 1 1 1 1 6 190 0) (3 537 1 0 41 1 0 78 0) (9 537 1 0 41 1 0 210 0) (27 537 1 0 41 1 1 77 0) (2 537 1 0 41 1 0 56 0) (6 537 1 0 41 1 0 144 0) (18 537 1 0 41 1 1 77 0) (54 537 1 0 41 1 1 143 0) (4 537 1 0 41 1 0 100 0) (12 537 1 0 41 1 0 276 0) (36 537 1 0 41 1 1 77 0) (108 537 1 0 41 1 1 209 0))
\ No newline at end of file
# NAMD extended system configuration output file
#$LABELS step a_x a_y a_z b_x b_y b_z c_x c_y c_z o_x o_y o_z
500 106.961377282 0 0 0 106.961377282 0 0 0 76.4009837728 0 0 0
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set temperature 300 ;# target temperature used several times below
cellBasisVector1 108.8612 0.0 0.0
cellBasisVector2 0.0 108.8612 0.0
cellBasisVector3 0.0 0.0 77.758
cellOrigin 0.0 0.0 0.0
coordinates apoa1.pdb
temperature $temperature
seed 74269
# Constant Temperature Control
#langevin on ;# langevin dynamics
#langevinDamping 1. ;# damping coefficient of 1/ps
#langevinTemp $temperature ;# random noise at this level
#langevinHydrogen no ;# don't couple bath to hydrogens
loweAndersen on
loweAndersenTemp $temperature
# Constant Pressure Control (variable volume)
useGroupPressure yes ;# needed for rigid bonds
useFlexibleCell no ;# no for water box, yes for membrane
useConstantArea no ;# no for water box, maybe for membrane
#langevinPiston on
#langevinPistonTarget 1.01325 ;# pressure in bar -> 1 atm
#langevinPistonPeriod 100. ;# oscillation period around 100 fs
#langevinPistonDecay 50. ;# oscillation decay time of 50 fs
#langevinPistonTemp $temperature ;# coupled to heat bath
BerendsenPressure on
BerendsenPressureTarget 1.01325
BerendsenPressureCompressibility 4.57E-5
BerendsenPressureRelaxationTime 100.
BerendsenPressureFreq 20
switching on
switchdist 10
cutoff 12
pairlistdist 13.5
margin 0
stepspercycle 20
PME on
PMEGridSizeX 108
PMEGridSizeY 108
PMEGridSizeZ 80
structure apoa1.psf
parameters par_all22_prot_lipid.xplor
parameters par_all22_popc.xplor
exclude scaled1-4
1-4scaling 1.0
timestep 1.0
fullElectFrequency 4
numsteps 500
outputtiming 20
outputname apoa1-out
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REMARKS Additional POPC parameters guessed by Jim Phillips
REMARKS FILENAME="par_all22_popc.xplor"
ANGLE CEL1 CEL1 CTL2 48.00 124.00 ! JCP guess 3/97
ANGLE CEL1 CTL2 CTL2 32.00 112.00 ! JCP guess 3/97
DIHEDRAL CEL1 CEL1 CTL2 CTL2 0.5000 3 0.00 ! JCP guess 3/97
DIHEDRAL HAL1 CEL1 CTL2 CTL2 0.1200 3 0.00 ! JCP guess 3/97
DIHEDRAL CEL1 CEL1 CTL2 HAL 0.1200 3 0.00 ! JCP guess 3/97
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(FFTW-2.1.3 (108 537 1 0 123 1 1 209 0) (36 537 1 0 123 1 1 77 0) (12 537 1 0 123 1 0 276 0) (4 537 1 0 123 1 0 100 0) (54 537 1 0 123 1 1 143 0) (18 537 1 0 123 1 1 77 0) (6 537 1 0 123 1 0 144 0) (2 537 1 0 123 1 0 56 0) (27 537 1 0 123 1 1 77 0) (9 537 1 0 123 1 0 210 0) (3 537 1 0 123 1 0 78 0) (108 537 1 0 287 1 1 209 0) (36 537 1 0 287 1 1 77 0) (12 537 1 0 287 1 0 276 0) (4 537 1 0 287 1 0 100 0) (54 537 1 0 287 1 1 209 0) (18 537 1 0 287 1 1 77 0) (6 537 1 0 287 1 0 144 0) (2 537 1 0 287 1 0 56 0) (27 537 1 0 287 1 1 77 0) (9 537 1 0 287 1 0 210 0) (3 537 1 0 287 1 0 78 0) (108 537 -1 0 123 1 1 198 0) (36 537 -1 0 123 1 1 66 0) (12 537 -1 0 123 1 0 265 0) (4 537 -1 0 123 1 0 89 0) (54 537 -1 0 123 1 1 198 0) (18 537 -1 0 123 1 1 66 0) (6 537 -1 0 123 1 0 133 0) (2 537 -1 0 123 1 0 45 0) (27 537 -1 0 123 1 1 66 0) (9 537 -1 0 123 1 0 199 0) (3 537 -1 0 123 1 0 67 0) (108 537 -1 0 287 1 1 198 0) (36 537 -1 0 287 1 1 66 0) (12 537 -1 0 287 1 0 265 0) (4 537 -1 0 287 1 0 89 0) (54 537 -1 0 287 1 1 198 0) (18 537 -1 0 287 1 1 66 0) (6 537 -1 0 287 1 0 133 0) (2 537 -1 0 287 1 0 45 0) (27 537 -1 0 287 1 1 66 0) (9 537 -1 0 287 1 0 199 0) (3 537 -1 0 287 1 0 67 0) (5 529 -1 1 1 1 4 112 0) (2 529 -1 1 1 1 4 46 0) (10 529 -1 1 1 1 4 222 0) (4 529 -1 1 1 1 4 90 0) (20 529 -1 1 1 1 6 47 0) (8 529 -1 1 1 1 4 178 0) (40 529 -1 1 1 1 6 91 0) (16 529 -1 1 1 1 4 354 0) (80 529 -1 1 1 1 6 113 0) (3 537 -1 0 41 1 0 67 0) (9 537 -1 0 41 1 0 199 0) (27 537 -1 0 41 1 1 66 0) (2 537 -1 0 41 1 0 45 0) (6 537 -1 0 41 1 0 133 0) (18 537 -1 0 41 1 1 66 0) (54 537 -1 0 41 1 1 198 0) (4 537 -1 0 41 1 0 89 0) (12 537 -1 0 41 1 0 265 0) (36 537 -1 0 41 1 1 132 0) (108 537 -1 0 41 1 1 198 0) (3 537 -1 0 1107 1 0 67 0) (9 537 -1 0 1107 1 0 199 0) (27 537 -1 0 1107 1 1 66 0) (2 537 -1 0 1107 1 0 45 0) (6 537 -1 0 1107 1 0 133 0) (18 537 -1 0 1107 1 1 66 0) (54 537 -1 0 1107 1 1 198 0) (4 537 -1 0 1107 1 0 89 0) (12 537 -1 0 1107 1 0 265 0) (36 537 -1 0 1107 1 1 66 0) (108 537 -1 0 1107 1 1 198 0) (3 537 1 0 1107 1 0 78 0) (9 537 1 0 1107 1 0 210 0) (27 537 1 0 1107 1 1 77 0) (2 537 1 0 1107 1 0 56 0) (6 537 1 0 1107 1 0 144 0) (18 537 1 0 1107 1 1 77 0) (54 537 1 0 1107 1 1 209 0) (4 537 1 0 1107 1 0 100 0) (12 537 1 0 1107 1 0 276 0) (36 537 1 0 1107 1 1 77 0) (108 537 1 0 1107 1 1 209 0) (5 529 1 1 1 1 5 125 0) (2 529 1 1 1 1 5 59 0) (10 529 1 1 1 1 5 235 0) (4 529 1 1 1 1 5 103 0) (20 529 1 1 1 1 6 58 0) (8 529 1 1 1 1 5 191 0) (40 529 1 1 1 1 6 102 0) (16 529 1 1 1 1 5 367 0) (80 529 1 1 1 1 6 234 0) (3 537 1 0 41 1 0 78 0) (9 537 1 0 41 1 0 210 0) (27 537 1 0 41 1 1 77 0) (2 537 1 0 41 1 0 56 0) (6 537 1 0 41 1 0 144 0) (18 537 1 0 41 1 1 77 0) (54 537 1 0 41 1 1 209 0) (4 537 1 0 41 1 0 100 0) (12 537 1 0 41 1 0 276 0) (36 537 1 0 41 1 1 77 0) (108 537 1 0 41 1 1 209 0))
\ No newline at end of file
# NAMD extended system configuration output file
#$LABELS step a_x a_y a_z b_x b_y b_z c_x c_y c_z o_x o_y o_z
500 108.8612 0 0 0 108.8612 0 0 0 77.758 0 0 0
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cellBasisVector1 108.8612 0.0 0.0
cellBasisVector2 0.0 108.8612 0.0
cellBasisVector3 0.0 0.0 77.758
cellOrigin 0.0 0.0 0.0
coordinates apoa1.pdb
temperature 300
seed 74269
switching on
switchdist 10
cutoff 12
pairlistdist 13.5
margin 0
stepspercycle 20
PME on
PMEGridSizeX 108
PMEGridSizeY 108
PMEGridSizeZ 80
structure apoa1.psf
parameters par_all22_prot_lipid.xplor
parameters par_all22_popc.xplor
exclude scaled1-4
1-4scaling 1.0
timestep 1.0
fullElectFrequency 4
numsteps 500
outputtiming 20
outputname apoa1-out
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REMARKS Additional POPC parameters guessed by Jim Phillips
REMARKS FILENAME="par_all22_popc.xplor"
ANGLE CEL1 CEL1 CTL2 48.00 124.00 ! JCP guess 3/97
ANGLE CEL1 CTL2 CTL2 32.00 112.00 ! JCP guess 3/97
DIHEDRAL CEL1 CEL1 CTL2 CTL2 0.5000 3 0.00 ! JCP guess 3/97
DIHEDRAL HAL1 CEL1 CTL2 CTL2 0.1200 3 0.00 ! JCP guess 3/97
DIHEDRAL CEL1 CEL1 CTL2 HAL 0.1200 3 0.00 ! JCP guess 3/97
This diff is collapsed.
(FFTW-2.1.3 (108 537 1 0 123 1 1 209 0) (36 537 1 0 123 1 1 77 0) (12 537 1 0 123 1 0 276 0) (4 537 1 0 123 1 0 100 0) (54 537 1 0 123 1 1 143 0) (18 537 1 0 123 1 1 77 0) (6 537 1 0 123 1 0 144 0) (2 537 1 0 123 1 0 56 0) (27 537 1 0 123 1 1 77 0) (9 537 1 0 123 1 0 210 0) (3 537 1 0 123 1 0 78 0) (108 537 1 0 287 1 1 209 0) (36 537 1 0 287 1 1 77 0) (12 537 1 0 287 1 0 276 0) (4 537 1 0 287 1 0 100 0) (54 537 1 0 287 1 1 209 0) (18 537 1 0 287 1 1 77 0) (6 537 1 0 287 1 0 144 0) (2 537 1 0 287 1 0 56 0) (27 537 1 0 287 1 1 77 0) (9 537 1 0 287 1 0 210 0) (3 537 1 0 287 1 0 78 0) (108 537 -1 0 123 1 1 198 0) (36 537 -1 0 123 1 1 66 0) (12 537 -1 0 123 1 0 265 0) (4 537 -1 0 123 1 0 89 0) (54 537 -1 0 123 1 1 198 0) (18 537 -1 0 123 1 1 66 0) (6 537 -1 0 123 1 0 133 0) (2 537 -1 0 123 1 0 45 0) (27 537 -1 0 123 1 1 66 0) (9 537 -1 0 123 1 0 199 0) (3 537 -1 0 123 1 0 67 0) (108 537 -1 0 287 1 1 198 0) (36 537 -1 0 287 1 1 66 0) (12 537 -1 0 287 1 0 265 0) (4 537 -1 0 287 1 0 89 0) (54 537 -1 0 287 1 1 198 0) (18 537 -1 0 287 1 1 66 0) (6 537 -1 0 287 1 0 133 0) (2 537 -1 0 287 1 0 45 0) (27 537 -1 0 287 1 1 66 0) (9 537 -1 0 287 1 0 199 0) (3 537 -1 0 287 1 0 67 0) (5 529 -1 1 1 1 4 112 0) (2 529 -1 1 1 1 4 46 0) (10 529 -1 1 1 1 4 222 0) (4 529 -1 1 1 1 4 90 0) (20 529 -1 1 1 1 6 47 0) (8 529 -1 1 1 1 4 178 0) (40 529 -1 1 1 1 6 91 0) (16 529 -1 1 1 1 4 354 0) (80 529 -1 1 1 1 6 113 0) (3 537 -1 0 41 1 0 67 0) (9 537 -1 0 41 1 0 199 0) (27 537 -1 0 41 1 1 66 0) (2 537 -1 0 41 1 0 45 0) (6 537 -1 0 41 1 0 133 0) (18 537 -1 0 41 1 1 66 0) (54 537 -1 0 41 1 1 198 0) (4 537 -1 0 41 1 0 89 0) (12 537 -1 0 41 1 0 265 0) (36 537 -1 0 41 1 1 132 0) (108 537 -1 0 41 1 1 198 0) (3 537 -1 0 1107 1 0 67 0) (9 537 -1 0 1107 1 0 199 0) (27 537 -1 0 1107 1 1 66 0) (2 537 -1 0 1107 1 0 45 0) (6 537 -1 0 1107 1 0 133 0) (18 537 -1 0 1107 1 1 66 0) (54 537 -1 0 1107 1 1 198 0) (4 537 -1 0 1107 1 0 89 0) (12 537 -1 0 1107 1 0 265 0) (36 537 -1 0 1107 1 1 66 0) (108 537 -1 0 1107 1 1 198 0) (3 537 1 0 1107 1 0 78 0) (9 537 1 0 1107 1 0 210 0) (27 537 1 0 1107 1 1 77 0) (2 537 1 0 1107 1 0 56 0) (6 537 1 0 1107 1 0 144 0) (18 537 1 0 1107 1 1 77 0) (54 537 1 0 1107 1 1 209 0) (4 537 1 0 1107 1 0 100 0) (12 537 1 0 1107 1 0 276 0) (36 537 1 0 1107 1 1 77 0) (108 537 1 0 1107 1 1 209 0) (5 529 1 1 1 1 5 125 0) (2 529 1 1 1 1 5 59 0) (10 529 1 1 1 1 5 235 0) (4 529 1 1 1 1 5 103 0) (20 529 1 1 1 1 6 58 0) (8 529 1 1 1 1 5 191 0) (40 529 1 1 1 1 6 102 0) (16 529 1 1 1 1 5 367 0) (80 529 1 1 1 1 6 234 0) (3 537 1 0 41 1 0 78 0) (9 537 1 0 41 1 0 210 0) (27 537 1 0 41 1 1 77 0) (2 537 1 0 41 1 0 56 0) (6 537 1 0 41 1 0 144 0) (18 537 1 0 41 1 1 77 0) (54 537 1 0 41 1 1 209 0) (4 537 1 0 41 1 0 100 0) (12 537 1 0 41 1 0 276 0) (36 537 1 0 41 1 1 77 0) (108 537 1 0 41 1 1 209 0) (3 537 -1 0 4428 1 0 67 0) (9 537 -1 0 4428 1 0 199 0) (27 537 -1 0 4428 1 1 66 0) (2 537 -1 0 4428 1 0 45 0) (6 537 -1 0 4428 1 0 133 0) (18 537 -1 0 4428 1 1 66 0) (54 537 -1 0 4428 1 1 198 0) (4 537 -1 0 4428 1 0 89 0) (12 537 -1 0 4428 1 0 265 0) (36 537 -1 0 4428 1 1 66 0) (108 537 -1 0 4428 1 1 198 0) (3 537 1 0 4428 1 0 78 0) (9 537 1 0 4428 1 0 210 0) (27 537 1 0 4428 1 1 77 0) (2 537 1 0 4428 1 0 56 0) (6 537 1 0 4428 1 0 144 0) (18 537 1 0 4428 1 1 77 0) (54 537 1 0 4428 1 1 209 0) (4 537 1 0 4428 1 0 100 0) (12 537 1 0 4428 1 0 276 0) (36 537 1 0 4428 1 1 77 0) (108 537 1 0 4428 1 1 209 0))
\ No newline at end of file
# NAMD extended system configuration restart file
#$LABELS step a_x a_y a_z b_x b_y b_z c_x c_y c_z o_x o_y o_z
500 108.8612 0 0 0 108.8612 0 0 0 77.758 0 0 0
# NAMD extended system configuration restart file
#$LABELS step a_x a_y a_z b_x b_y b_z c_x c_y c_z o_x o_y o_z
400 108.8612 0 0 0 108.8612 0 0 0 77.758 0 0 0
# NAMD extended system configuration output file
#$LABELS step a_x a_y a_z b_x b_y b_z c_x c_y c_z o_x o_y o_z
500 108.8612 0 0 0 108.8612 0 0 0 77.758 0 0 0
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cellBasisVector1 108.8612 0.0 0.0
cellBasisVector2 0.0 108.8612 0.0
cellBasisVector3 0.0 0.0 77.758
cellOrigin 0.0 0.0 0.0
coordinates apoa1.pdb
temperature 300
seed 74269
switching on
switchdist 10
cutoff 12
pairlistdist 13.5
margin 0
stepspercycle 20
PME on
PMEGridSizeX 108
PMEGridSizeY 108
PMEGridSizeZ 80
structure apoa1.psf
parameters par_all22_prot_lipid.xplor
parameters par_all22_popc.xplor
exclude scaled1-4
1-4scaling 1.0
timestep 1.0
fullElectFrequency 4
numsteps 500
outputtiming 20
outputname apoa1-out
outputEnergies 20 # Energy output frequency
restartfreq 100 # Restart file frequency
DCDfreq 20 # Trajectory file frequency
velDCDfreq 50 # Trajectory file frequency
forceDCDfreq 100 # Trajectory file frequency
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REMARKS Additional POPC parameters guessed by Jim Phillips
REMARKS FILENAME="par_all22_popc.xplor"
ANGLE CEL1 CEL1 CTL2 48.00 124.00 ! JCP guess 3/97
ANGLE CEL1 CTL2 CTL2 32.00 112.00 ! JCP guess 3/97
DIHEDRAL CEL1 CEL1 CTL2 CTL2 0.5000 3 0.00 ! JCP guess 3/97
DIHEDRAL HAL1 CEL1 CTL2 CTL2 0.1200 3 0.00 ! JCP guess 3/97
DIHEDRAL CEL1 CEL1 CTL2 HAL 0.1200 3 0.00 ! JCP guess 3/97
This diff is collapsed.
(FFTW-2.1.3 (108 537 1 0 123 1 1 209 0) (36 537 1 0 123 1 1 77 0) (12 537 1 0 123 1 0 276 0) (4 537 1 0 123 1 0 100 0) (54 537 1 0 123 1 1 143 0) (18 537 1 0 123 1 1 77 0) (6 537 1 0 123 1 0 144 0) (2 537 1 0 123 1 0 56 0) (27 537 1 0 123 1 1 77 0) (9 537 1 0 123 1 0 210 0) (3 537 1 0 123 1 0 78 0) (108 537 1 0 287 1 1 209 0) (36 537 1 0 287 1 1 77 0) (12 537 1 0 287 1 0 276 0) (4 537 1 0 287 1 0 100 0) (54 537 1 0 287 1 1 209 0) (18 537 1 0 287 1 1 77 0) (6 537 1 0 287 1 0 144 0) (2 537 1 0 287 1 0 56 0) (27 537 1 0 287 1 1 77 0) (9 537 1 0 287 1 0 210 0) (3 537 1 0 287 1 0 78 0) (108 537 -1 0 123 1 1 198 0) (36 537 -1 0 123 1 1 66 0) (12 537 -1 0 123 1 0 265 0) (4 537 -1 0 123 1 0 89 0) (54 537 -1 0 123 1 1 198 0) (18 537 -1 0 123 1 1 66 0) (6 537 -1 0 123 1 0 133 0) (2 537 -1 0 123 1 0 45 0) (27 537 -1 0 123 1 1 66 0) (9 537 -1 0 123 1 0 199 0) (3 537 -1 0 123 1 0 67 0) (108 537 -1 0 287 1 1 198 0) (36 537 -1 0 287 1 1 66 0) (12 537 -1 0 287 1 0 265 0) (4 537 -1 0 287 1 0 89 0) (54 537 -1 0 287 1 1 198 0) (18 537 -1 0 287 1 1 66 0) (6 537 -1 0 287 1 0 133 0) (2 537 -1 0 287 1 0 45 0) (27 537 -1 0 287 1 1 66 0) (9 537 -1 0 287 1 0 199 0) (3 537 -1 0 287 1 0 67 0) (5 529 -1 1 1 1 4 112 0) (2 529 -1 1 1 1 4 46 0) (10 529 -1 1 1 1 4 222 0) (4 529 -1 1 1 1 4 90 0) (20 529 -1 1 1 1 6 47 0) (8 529 -1 1 1 1 4 178 0) (40 529 -1 1 1 1 6 91 0) (16 529 -1 1 1 1 4 354 0) (80 529 -1 1 1 1 6 113 0) (3 537 -1 0 41 1 0 67 0) (9 537 -1 0 41 1 0 199 0) (27 537 -1 0 41 1 1 66 0) (2 537 -1 0 41 1 0 45 0) (6 537 -1 0 41 1 0 133 0) (18 537 -1 0 41 1 1 66 0) (54 537 -1 0 41 1 1 198 0) (4 537 -1 0 41 1 0 89 0) (12 537 -1 0 41 1 0 265 0) (36 537 -1 0 41 1 1 132 0) (108 537 -1 0 41 1 1 198 0) (3 537 -1 0 1107 1 0 67 0) (9 537 -1 0 1107 1 0 199 0) (27 537 -1 0 1107 1 1 66 0) (2 537 -1 0 1107 1 0 45 0) (6 537 -1 0 1107 1 0 133 0) (18 537 -1 0 1107 1 1 66 0) (54 537 -1 0 1107 1 1 198 0) (4 537 -1 0 1107 1 0 89 0) (12 537 -1 0 1107 1 0 265 0) (36 537 -1 0 1107 1 1 66 0) (108 537 -1 0 1107 1 1 198 0) (3 537 1 0 1107 1 0 78 0) (9 537 1 0 1107 1 0 210 0) (27 537 1 0 1107 1 1 77 0) (2 537 1 0 1107 1 0 56 0) (6 537 1 0 1107 1 0 144 0) (18 537 1 0 1107 1 1 77 0) (54 537 1 0 1107 1 1 209 0) (4 537 1 0 1107 1 0 100 0) (12 537 1 0 1107 1 0 276 0) (36 537 1 0 1107 1 1 77 0) (108 537 1 0 1107 1 1 209 0) (5 529 1 1 1 1 5 125 0) (2 529 1 1 1 1 5 59 0) (10 529 1 1 1 1 5 235 0) (4 529 1 1 1 1 5 103 0) (20 529 1 1 1 1 6 58 0) (8 529 1 1 1 1 5 191 0) (40 529 1 1 1 1 6 102 0) (16 529 1 1 1 1 5 367 0) (80 529 1 1 1 1 6 234 0) (3 537 1 0 41 1 0 78 0) (9 537 1 0 41 1 0 210 0) (27 537 1 0 41 1 1 77 0) (2 537 1 0 41 1 0 56 0) (6 537 1 0 41 1 0 144 0) (18 537 1 0 41 1 1 77 0) (54 537 1 0 41 1 1 209 0) (4 537 1 0 41 1 0 100 0) (12 537 1 0 41 1 0 276 0) (36 537 1 0 41 1 1 77 0) (108 537 1 0 41 1 1 209 0) (3 537 -1 0 4428 1 0 67 0) (9 537 -1 0 4428 1 0 199 0) (27 537 -1 0 4428 1 1 66 0) (2 537 -1 0 4428 1 0 45 0) (6 537 -1 0 4428 1 0 133 0) (18 537 -1 0 4428 1 1 66 0) (54 537 -1 0 4428 1 1 198 0) (4 537 -1 0 4428 1 0 89 0) (12 537 -1 0 4428 1 0 265 0) (36 537 -1 0 4428 1 1 66 0) (108 537 -1 0 4428 1 1 198 0) (3 537 1 0 4428 1 0 78 0) (9 537 1 0 4428 1 0 210 0) (27 537 1 0 4428 1 1 77 0) (2 537 1 0 4428 1 0 56 0) (6 537 1 0 4428 1 0 144 0) (18 537 1 0 4428 1 1 77 0) (54 537 1 0 4428 1 1 209 0) (4 537 1 0 4428 1 0 100 0) (12 537 1 0 4428 1 0 276 0) (36 537 1 0 4428 1 1 77 0) (108 537 1 0 4428 1 1 209 0))
\ No newline at end of file
# NAMD extended system configuration restart file
#$LABELS step a_x a_y a_z b_x b_y b_z c_x c_y c_z o_x o_y o_z
500 108.8612 0 0 0 108.8612 0 0 0 77.758 0 0 0
# NAMD extended system configuration restart file
#$LABELS step a_x a_y a_z b_x b_y b_z c_x c_y c_z o_x o_y o_z
450 108.8612 0 0 0 108.8612 0 0 0 77.758 0 0 0
# NAMD extended system configuration output file
#$LABELS step a_x a_y a_z b_x b_y b_z c_x c_y c_z o_x o_y o_z
500 108.8612 0 0 0 108.8612 0 0 0 77.758 0 0 0
# NAMD extended system configuration output file
#$LABELS step a_x a_y a_z b_x b_y b_z c_x c_y c_z o_x o_y o_z
500 108.8612 0 0 0 108.8612 0 0 0 77.758 0 0 0
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cellBasisVector1 108.8612 0.0 0.0
cellBasisVector2 0.0 108.8612 0.0
cellBasisVector3 0.0 0.0 77.758
cellOrigin 0.0 0.0 0.0
coordinates apoa1.pdb
temperature 300
seed 74269
switching on
switchdist 10
cutoff 12
pairlistdist 13.5
margin 0
stepspercycle 20
PME on
PMEGridSizeX 108
PMEGridSizeY 108
PMEGridSizeZ 80
structure apoa1.psf
parameters par_all22_prot_lipid.xplor
parameters par_all22_popc.xplor
exclude scaled1-4
1-4scaling 1.0
timestep 1.0
fullElectFrequency 4
numsteps 500
outputtiming 20
outputname apoa1-out
outputEnergies 20 # Energy output frequency
restartfreq 50 # Restart file frequency
DCDfreq 100 # Trajectory file frequency
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This diff is collapsed.
REMARKS Additional POPC parameters guessed by Jim Phillips
REMARKS FILENAME="par_all22_popc.xplor"
ANGLE CEL1 CEL1 CTL2 48.00 124.00 ! JCP guess 3/97
ANGLE CEL1 CTL2 CTL2 32.00 112.00 ! JCP guess 3/97
DIHEDRAL CEL1 CEL1 CTL2 CTL2 0.5000 3 0.00 ! JCP guess 3/97
DIHEDRAL HAL1 CEL1 CTL2 CTL2 0.1200 3 0.00 ! JCP guess 3/97
DIHEDRAL CEL1 CEL1 CTL2 HAL 0.1200 3 0.00 ! JCP guess 3/97
This diff is collapsed.
BPTI Interactive Simulation
First start NAMD with bpti.namd, then start VMD as "vmd -e bpti.vmd" to
connect and view the simulation. You may need to edit the command
"imd connect localhost 3111" with the correct hostname, or just type
the correct version in the VMD console.
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# NAMD configuration file for BPTI
# molecular system
structure bpti.psf
# force field
paratypecharmm on
parameters par_all22_prot.inp
exclude scaled1-4
1-4scaling 1.0
# approximations
switching on
switchdist 8
cutoff 12
pairlistdist 13.5
margin 0
stepspercycle 20
#integrator
timestep 1.0
#output
outputenergies 10
outputtiming 100
binaryoutput no
imdon yes
imdfreq 1
imdport 3111
# molecular system
coordinates bpti.pdb
#output
outputname bpti_out
#dcdfreq 1000
#protocol
temperature 0
langevin on
langevinDamping 10
langevinTemp 300
#script
minimize 200
run 20000
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