parmed.amber.mdin.mdin module

This module will create an amber mdin file for either sander or pmemd (or others). The program specification loads the appropriate dictionaries with default values, etc. It can read and write mdins.

GPL LICENSE INFO

Copyright (C) 2009 - 2014 Dwight Mcgee, Bill Miller III, and Jason Swails

This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.

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

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')

SHAKE()

TI(clambda=0.0)

change(namelist, variable, value)

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

check()

constPressure(press=1.0, taup=1.0)

constTemp(ntt=3, temp=300.0, gamma_ln=2.0, ig=- 1, tautp=1.0)

constVolume()

constpH(solvph=7.0, igb=2, ntcnstph=10)

genBorn(igb=5, rgbmax=25.0)

heat(tempi=0.0, temp0=300.0, ntt=3, tautp=5.0, ig=- 1, gamma_ln=5.0)

minimization(imin=1, maxcyc=1, ncyc=10, ntmin=1)

read(filename='mdin')

restart(ntx=5)

restrainBackbone(restraint_wt=0.0)

restrainHeavyAtoms(restraint_wt=0.0)

softcore_TI(scalpha=0.5, scmask='', crgmask='', logdvdl=0)

time(time=1000.0, dt=- 1)

write(filename='mdin')

parmed.amber.mdin.mdin.addOn(line, string, file)