MMTSB
Tool Set Documentation

NAMD Parameters

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bomlevundefset bomb level
prnlevundefset print level
 
param36parameter set: 19 (CHARMM19), 22 (CHARMM22), opls, a94 (amber 94), eef1, mmff
xparundefextra parameter files
 
 
cmap1use CMAP correction
geomvdwundefgeometric combination of sigmas for OPLS L-J terms
scale141.01-4 scaling
 
epsilon1.0dielectric constant for non-bonded interactions
cutnbundefcutoff for non-bonded list generation
cutoffundefcutoff for non-bonded interactions
cutonundefonset of switching function for non-bonded interaction
cut1use cutoff
truncundefshift/fshift/switch/fswitch
 
shake0use shake
shaketol1.0E-8shake tolerance
 
periodic1use periodic boundaries
ewald1use Ewald for explicit solvent
npmeundef64, # number of grid points for PME grid
npmexundefnumber of grid points in x direction
npmeyundefnumber of grid points in y direction
npmezundefnumber of grid points in z direction
pmegridundefpme grid spacing
marginundefpatch margin
ldb1load balancing
 
boxshapeundefbox shape for periodic boundaries
boxsizeundefbox size
boxxundefbox x dimension
boxyundefbox y dimension
boxzundefbox z dimension
 
dynens'NVT'dynamics ensemble 'NVT', 'NPT', 'NPH', 'NVE'
dynber0use Berendsen thermostat
tcouplefileundeffile with Berendsen time constant
dyntstep0.002dynamics time step in picoseconds
dynsteps100dynamics steps
dyntemp298dynamics temperature
dynseedundefdynamics random seed
dyntrfrqundeftrans/rot removal frequency
dynremovecomundefremove center of mass motion when restarting
dyneqfrq0velocity reassignment frequency
dynscalefrq0temperature rescaling frequency
dynoutfrq500frequency of energy/trajectory output
dynouttime1000frequency of writing timing information
dynrestfrq1000frequency of saving restart files
dyneoutfrqundeffrequency of writing out energy information
dynupdnb10update of non-bonded list
dynpress1.00the pressure (in atm) for NPT simulations
dynpperiod200.0gamma value for NPT simulations
dynpdecay100.0Langevin piston mass for NPT simulations
dynnpat0constant surface area for membrane simulations
 
lang1flag for running Langevin dynamics
langBAOAB0BAOAB integrator from Leimkuhler et al.
langfbeta1.0friction coefficient for Langevin dynamics
 
tmdrmsdundefset initial TMD RMSD to turn it on
tmdrmsdtoundefset final TMD RMSD, by default equal to initial RMSD
tmdk100force constant
tmdoutfrqundefTMD output frequency
tmdrefundefTMD reference file
 
tmdrmsd2undefset initial TMD RMSD to turn it on
tmdrmsd2toundefset final TMD RMSD, by default equal to initial RMSD
tmdk2100force constant
tmdref2undefTMD reference file
 
mmtsbserverundefMMSTB server host name
mmtsbportundefMMTSB server port number
mmtsbsidundefMMTSB server ID
mmtsbjobidundefMMTSB job ID
mmtsbcycleundefreplica exchange cycle length
 
cons0set to 1 and provide reference file through -consref
 
colvarsundefturn on and provide config file for colvars
 
extrabondsundefturn on and provide extra bonds input file
 
minstepsundefminimize