Dear Dr. Dodson
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
smd.txt
#
# MD time (ps), CV, handle_position, spring_constant, work
#
50.0000 1.49452542 1.42000000 1000.00000000
0.00000000
52.5000 1.09928957 1.15300000 1000.00000000
0.73671660
55.0000 0.82355211 0.88600000 1000.00000000
1.45414492
57.5000 0.66830655 0.61900000 1000.00000000
2.73445986
60.0000 0.41748331 0.35200000 1000.00000000
5.04733323
62.5000 0.01930706 0.08500000 1000.00000000
6.98244045
65.0000 -0.13774148 -0.18200000 1000.00000000
6.30370813
67.5000 -0.43998671 -0.44900000 1000.00000000
3.24075496
70.0000 -0.67032144 -0.71600000 1000.00000000
-0.81911976
72.5000 -1.06095224 -0.98300000 1000.00000000
-3.44306421
#
#
<> total work done: -4.2166710649
#
Can you help me to solve the problem?
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Received on Tue May 14 2013 - 06:30:02 PDT
