parmed.amber.mdin package

Module contents

class parmed.amber.mdin.Mdin(program='sander', verbosity=1)[source]

Bases: object

Methods

change(namelist, variable, value)

Change the value of a variable without adding a new key-pair

AddCard

SHAKE

TI

check

constPressure

constTemp

constVolume

constpH

genBorn

heat

minimization

read

restart

restrainBackbone

restrainHeavyAtoms

softcore_TI

time

write
AddCard(title='Residues in card', cardString='RES 1')[source]
SHAKE()[source]
TI(clambda=0.0)[source]
change(namelist, variable, value)[source]

Change the value of a variable without adding a new key-pair

check()[source]
constPressure(press=1.0, taup=1.0)[source]
constTemp(ntt=3, temp=300.0, gamma_ln=2.0, ig=- 1, tautp=1.0)[source]
constVolume()[source]
constpH(solvph=7.0, igb=2, ntcnstph=10)[source]
genBorn(igb=5, rgbmax=25.0)[source]
heat(tempi=0.0, temp0=300.0, ntt=3, tautp=5.0, ig=- 1, gamma_ln=5.0)[source]
minimization(imin=1, maxcyc=1, ncyc=10, ntmin=1)[source]
read(filename='mdin')[source]
restart(ntx=5)[source]
restrainBackbone(restraint_wt=0.0)[source]
restrainHeavyAtoms(restraint_wt=0.0)[source]
softcore_TI(scalpha=0.5, scmask='', crgmask='', logdvdl=0)[source]
time(time=1000.0, dt=- 1)[source]
write(filename='mdin')[source]