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qm_mm_setup_for_reaction_coordinate_amber17

QM/MM setup for reaction coordinates (Amber16)

  • See section 21.6.2. of the manual of Amber17http://ambermd.org/doc12/Amber17.pdf for the definition of reaction coordinates. There are some changes from the previous version of Amber14.
  • Remember to include the flag infe=1 in the &cntrl section and the &smd section.
  • Here you have an example of the shortening of a distance between atoms 1387 and 4980.

QMMM 20 ps
&cntrl
ntx = 5, irest = 1, ntxo = 1,
ntpr = 1000, ntwx =1000,
ntf = 1, ntb = 2, dielc = 1.0,
cut = 10., nsnb = 10,
imin = 0, ibelly = 0, iwrap = 1,
nstlim=10000, dt = 0.002,
temp0 = 300.0, tempi = 300.0,
ntt = 1, vlimit = 20.0,
ntp = 1,
ntc = 1, tol = 0.00001, pres0=1, comp=44.6,
jfastw=0, nscm=1000,
ifqnt=1,infe=1,
/
&qmmm
qmmask= “:317 | :88@CB,HB2,HB3,CG,HG2,HG3,CD,OE1,OE2,HE2”,
qmcharge=0,
qm_theory='DFTB3',
qmshake=0,
writepdb=1,
verbosity=4,
qmcut=15.,
printcharges = 1,
printdipole = 1,
peptide_corr = 0,
/
&smd
output_file = 'trial.txt'
output_freq = 10
cv_file= 'cv.in'
/

*Specify the reaction coordinate (former ncsu_smd section in the input for Amber14) in the file cv.in.

cv_file
&colvar
cv_type='DISTANCE'
cv_ni= 2
cv_i= 1387, 4980
npath=2,path=2.84,0.95,path_mode='LINES',
nharm=1,harm=1000
/

qm_mm_setup_for_reaction_coordinate_amber17.txt · Last modified: 2017/05/09 06:21 by root