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qm_mm_setup_for_reaction_coordinate

QM/MM setup - Reaction coordinate

General setup

  • Do not break polar atoms. Always Csp3-Csp3 bonds such as Cα-Cβ
  • Be careful when defining the sign in a LCOD:
  • ““i”” means the pairs of atoms that are involved in the reaction coordinate; can be more than 4 atoms.
  • ““r”” gives the coefficients of the linear combination (one for each two numbers in the i list). The sign defines the progress of a breaking (positive) or forming (negative) bond.
  • ““path” defines the reaction coordinate values in the initial state (a) and in the final state (b): path=(a,b).

Distance restraint

Distance restraint that modifies the distance between two atoms. In the path the X refers to the initial position of the atoms in the system.

5 ps of QMMM at 300 K
&cntrl
ntx = 5, irest = 1, ntrx = 1,
ntxo = 1, nmropt = 0,
ntpr = 100, ntwx =100,
ntf = 1, ntb = 2, dielc = 1.0,
cut = 9., nsnb = 10,
imin = 0, ibelly = 0, iwrap = 1,
nstlim = 10000, dt = 0.0005,
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
/
&qmmm
iqmatoms=157,158,159,160,161,162,163,164,271,272,273,274,275,276,277,278,279,280,281,282,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,1213,1214,1215,1216,1217,1218,1219,1220,1289,1290,1291,1292,1293,1294,1295,1296,1297,1298,1299,1585,1586,1587,1588,1589,1590,1591,1592,1593,1594,1595,1596,1622,1623,1624,1625,1626,1627,1628,1629,1702,1703,1704,1705,1706,1707,1708,1709,1710,1711,1712,1713,1776,1777,1778,1779,1780,1781,1782,1783,1784,1785,1786,1787,3706,3707,3708,3709,3710,3711,6952,6953,6954,6955,6956,6957,6958,6959,6960,6961,6962,6963,6964,6965,6966,6967,6968,6969,6970,6971,6972,6973,6990,6991,6992,49716,49717,49718,
qmcharge=+2, (Total charge of the QM part)
qm_theory='DFTB',
qmshake=0,
diag_routine=0,
dftb_telec=100,
qmcut=8.0,(Check you are defining a similar cut-off for MM part)
qmshake=0,
writepdb= 1,
/
ncsu_smd

output_file = 'PMF_rc.txt'
output_freq = 100

variable
type = DISTANCE
i = (6955,6956)
path = (X,2.0) Here is the X
harm = (1000.0) k=1000.0 for V=k(d-d0)
end variable

end ncsu_smd

Linear combination of distances for restraint

QMMM
&cntrl
ntx = 5, irest = 1, ntrx = 1,
ntxo = 1, nmropt = 0,
ntpr = 100, ntwx =100,
ntf = 1, ntb = 2, dielc = 1.0,
cut = 9., nsnb = 10,
imin = 0, ibelly = 0, iwrap = 1,
nstlim = 20000, dt = 0.0005,
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,
/
&qmmm
iqmatoms=157,158,159,160,161,162,163,164,271,272,273,274,275,276,277,278,279,280,281,282,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,1213,1214,1215,1216,1217,1218,1219,1220,1289,1290,1291,1292,1293,1294,1295,1296,1297,1298,1299,1585,1586,1587,1588,1589,1590,1591,1592,1593,1594,1595,1596,1622,1623,1624,1625,1626,1627,1628,1629,1702,1703,1704,1705,1706,1707,1708,1709,1710,1711,1712,1713,1776,1777,1778,1779,1780,1781,1782,1783,1784,1785,1786,1787,3706,3707,3708,3709,3710,3711,6952,6953,6954,6955,6956,6957,6958,6959,6960,6961,6962,6963,6964,6965,6966,6967,6968,6969,6970,6971,6972,6973,6990,6991,6992,49716,49717,49718,
qmcharge=+2,
qm_theory='DFTB',
qmshake=0,
diag_routine=0,
dftb_telec=100,
qmcut=9.0,
qmshake=0,
writepdb= 1,
&end
&wt
type='DUMPFREQ', istep1=5,
&end
&wt
type=“END”,
&end
DISANG=dist.dat
DUMPAVE=dist.lis
/
ncsu_smd

output_file = 'smd_1.txt'
output_freq = 100

variable
type = LCOD
i = (49716,49717,49717,3710)
r = (1.0,-1.0)
path = (-0.78,0.78)
harm = (1000.0)
end variable

output_file = 'smd_2.txt'
output_freq = 100

variable
type = LCOD
i = (367,368,368,49716)
r = (1.0,-1.0)
path = (-0.83,0.83)
harm = (750.0)
end variable

output_file = 'smd_3.txt'
output_freq = 100

variable
type = DISTANCE
i = (277,6962)
path = (2.80,2.80)
harm = (5.0)
end variable

output_file = 'smd_4.txt'
output_freq = 100

variable
type = DISTANCE
i = (6956,1590)
path = (2.0,2.0)
harm = (5.0)
end variable

end ncsu_smd

Example input files

qm_mm_setup_for_reaction_coordinate.txt · Last modified: 2016/03/07 14:23 by root