Hi,
The harm you used for the first CV is 1000, that is too large, always we
want small harmonic strength and slower pulling to make the transition to
be close to quasistatic process.
So try with smaller harm value and longer simulation time, and begin with
only one CV would be better to see the result.
Feng Pan
On Tue, Jul 12, 2016 at 4:02 AM, bharat gupta <bharat.85.monu.gmail.com>
wrote:
> Hello Amber Users,
>
> I am trying to perform a SMD for my reaction (inversion reaction in
> Glycoside Hydrolase) which involves:
>
> (i) a proton transfer from Base residue to the O4 atom glycosidic bond
> (C4-O4)
> (ii) breakage of C-O4 bond
> (iii) abstraction of proton from nearby water molecule by Acid residue to
> charge water for nucleophilic attack on C4 atom.
>
> I was able to perform SMD for the first two step but the energy is way too
> high the two reactions. Here's the link for the plots and the output file
> from SMD simulation:
> https://drive.google.com/open?id=0B6ehLXK0eP7scmRRcWRYRnBkOGs
>
> https://drive.google.com/open?id=0B6ehLXK0eP7sYmtMc1BBVFphZ2c
>
>
>
> Here's the setting files for the SMD:
>
> ===============
> QM/MM SMD
> &cntrl
> imin = 0,irest=0,ntx=1,
> ntb=2,pres0=1.0,ntp=1,taup=1.0,
> cut=20,ntr=0,
> ntc=1,ntf=1,tol=0.00001
> tempi=300.0,temp0=300.0,
> ntt=3, gamma_ln=1.0,
> nstlim=100000, dt=0.0005,
> ntpr=50, ntwx=50, ntwr=100,
> ifqnt=1
> /
> &qmmm
> qmmask='.2138-2143,2109-2114,7734-7740,8089-8154,30275-30277',
> qmcharge=-2,
> qm_theory='DFTB',
> qmcut=20,
> qmshake=0,
> writepdb=1
> /
> ncsu_smd
>
>
>
> output_file = 'smd3.txt'
>
> output_freq = 100
>
>
>
> variable
>
> type = LCOD ! Linear Combination of Distance # proton transfer step
>
> i = (8132,7740,7739,7740)
>
> r = (1.0,-1.0)
>
> path = (1.25,-1.25)
>
> harm = (1000.0)
>
> end variable
>
> variable
> type = DISTANCE ! Distance # glycosidic bond breakage
> i = (8122,8132)
> path = (X,3.0)
> harm = (50.0)
> end variable
> end ncsu_smd
> ==============================
>
> Could anybody tell me what could be the reason for such high energy values
> for the two steps? I am also confused about keeping the path value for
> proton transfer, what does the first and second values indicate in the path
> variable?
>
> Do I need to perform SMD for step (iii) as well for the entire reaction to
> happen or does the abstraction of H from water molecule should occur on its
> own, as it is a QM/MM simualtion?
>
> Thanks in advance for your suggestions.
>
> --
> *Best Regards*
> Bharat
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Feng Pan
Ph.D. Candidate
North Carolina State University
Department of Physics
Email: fpan3.ncsu.edu
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Received on Tue Jul 12 2016 - 10:30:03 PDT
