Hello,
I will try although I have been retired and no longer follow the AMBER
capabilities as closely as I did earlier in my career.
If I understand you correctly you are concerned about absolute magnitudes of
free energies calculated using the QMMM capabilities of AMBER12. Is that
correct? (I'm just restating this so you can be confident I understand your
question.) The actual values of free energies are not meaningful with MD
methods. Only free energy differences are meaningful. So proton transfer with
QMMM will allow you to calculate one side of a thermodynamic cycle, but the
values themselves are not meaningful, only their difference between them.
If I were to pursue this problem, I would draw the complete thermodynamic cycle
for the process (which might involve solvation effects, for example.) Then use
QMMM to calculate the unknown sides of the cycle. In most cases at least one
side will be known from experimental results.
You should also understand that the NCSU methods are no longer supported by the
AMBER developers. Only the SMD methods relying on NMR-style restraints are
supported.
Hope that helps,
Bud Dodson
On May 14, 2013, at 8:19 AM, Santi Tolosa wrote:
> 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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> http://lists.ambermd.org/mailman/listinfo/amber
--
M. L. Dodson
Business email: activesitedynamics-at-gmail-dot-com
Personal email: mldodson-at-comcast-dot-net
Gmail: mlesterdodson-at-gmail-dot-com
Phone: eight_three_two-five_63-386_one
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Received on Tue May 14 2013 - 07:00:02 PDT
