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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 Amber17 manual http://ambermd.org/doc12/Amber17.pdf for the definition of reaction coordinates. There are some IMPORTANT changes from the previous Amber14 version.
  • Remember to include the flag infe=1 in the &cntrl section and the (NEW) &smd section.
  • Here you have an example of how to shorten the distance between atoms 1387 and 4980 (i.e., bond creation).

QMMM 20 ps
&cntrl
ntx = 5, irest = 1, ntxo = 1,
ntpr = 1000, ntwx =1000,
ntf = 1, ntb = 2, dielc = 1.0,
cut = 9., nsnb = 10,
imin = 0, ibelly = 0, iwrap = 1,
nstlim=10000, dt = 0.002,\\amber16 nfe.pdf 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\\amber16 nfe.pdf output_file = 'trial.txt'
output_freq = 10
cv_file= 'cv.in'
/

*Specify the reaction coordinate (as done formerly in the ncsu_smd section of the Amber14 input file) in the external file cv.in.
Note that the “x” can no longer be used for the definition of the elements of the steering path, i.e. those elements must be real numbers!
BEWARE OF THE SYMBOL FOR THE INVERTED COMMA

Header for the 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: 2018/06/14 09:49 by root