I'm building the PMF of the proton transfer of amino acids in aqueous
solution with the SMD method (steered molecular dynamics) implemented in
Amber 12 program. We obtain a final energy (associated with the neutral
structure) of - 4 kcal/mol, more stable than the initial energy (associated
to the neutral structure), which does not seem logical. For them I am using
the files:
Mdin0
Glycine: qmmm equilibration MD
&cntrl
imin = 0,
irest = 0,
ntx = 1,
ntb = 1,
cut = 5.0,
tempi = 300.0,
temp0 = 300.0,
ntt = 1,
gamma_ln = 0.0,
ntf = 2, ntc = 2, tol = 0.00001,
dt = 0.0005,
ntpr = 50, ntwr=100, ntwx = 100,
nstlim = 100000,
ifqnt = 1,
nmropt = 1,
ibelly=1, bellymask=':WAT',
/
&qmmm
qmmask=':1',
qmcharge=0,
qm_theory='DFTB',
qmshake=0,
writepdb=1,
/
/
&wt type='DUMPFREQ', istep1 = 10,
/
&wt type='END',
/
DISANG=dist.RST
DUMPAVE=dist_vs_t
LISTIN=POUT
LISTOUT=POUT
Mdin1
Glycie: NCSU steered MD: LCOD rxn coord
&cntrl
imin = 0,
irest = 1,
ntx = 5,
ntb = 1,
cut = 5.0,
tempi = 300.0,
temp0 = 300.0,
ntt = 1,
gamma_ln = 0.0,
ntf = 2, ntc = 2, tol = 0.00001,
dt = 0.001,
ntpr = 100, ntwr=100, ntwx = 1000,
nstlim = 50000,
ifqnt = 1,
/
&qmmm
qmmask=':1',
qmcharge=0,
qm_theory='DFTB',
qmshake=0,
writepdb=1,
/
ncsu_smd
output_file = 'smd.txt'
output_freq = 500
variable
type = LCOD ! Linear Combination of Distance
i = (9,10,1,10)
r = (1.0,-1.0)
path = (1.42,-1.25) path_mode = LINES
harm = (1000.0)
end variable
end ncsu_smd
Can anyone help me to solve the problem?
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Received on Fri May 10 2013 - 04:30:02 PDT
