I don't have a specific answer to your question, but some ideas:
1) The NCSU modules are no longer actively supported, nor do I know of any
recent published uses of the ncsu_smd module. I think the preferred way to
do this in AMBER, at present, is with the 'jar' flag (it invokes the nmropt
module).
2) I don't know how accurate standard SCC-DFTB (now sometimes called DFTB2)
is for proton transfer, or even proton affinity. Are you using standard
parameters from the Elstner group? Are they validated for this kind of
calculation?
3) Your 'cut' value (and also 'qmcut') is *extremely* small. I have had a
hard time conserving energy with values below 8 (although I usually include
d-orbitals and set dt = 1fs, which doesn't help). I'm not an expert, but I
believe Jarzynski/Crooks type calculations are only meaningful if the
dynamics are deterministic, which will not be true if energy is not
conserved. You might consider turning on 'qmmm_switch' and increasing cut
to a more standard value (the default is 8).
4) I assume you meant to use Berendsen thermostat with a low frequency
coupling? You want to set 'tautp' in that case, not 'gamma_ln'.
Regards,
Brian
On Fri, May 10, 2013 at 7:05 AM, Santi Tolosa <santitolosa56.gmail.com>wrote:
> 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?
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Center for Integrative
Proteomics Room 308
Graduate Program in Chemical Physics : 174 Frelinghuysen Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
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Received on Fri May 10 2013 - 06:00:06 PDT
