Hi Vito,
I'm no expert by any means, but it seems like the code/simulation is
working. Perhaps your potential energy surface that you're looking at is
steeper than you thought? If there's a very sharp/high-energy region around
RC=-1.55 then -1.19 and -1.88 might be as close as your restraints can get
to sampling that region. You can turn up the restraint strength and see if
that gets you closer but realize that if this is the case that's Very high
energy positions. Also you might want to specify a more narrow window width
when dealing with such a drastic underlying free energy surface (i.e. do a
step size of maybe 0.04 instead of 0.2). That should give more information
about the nature of the barrier you're approaching. Hope this helps,
-Tim
On Fri, Oct 19, 2018 at 9:28 AM Vito GENNA <vito.genna.irbbarcelona.org>
wrote:
> Hi Zuo,
>
> You are right, there are 4 atoms but there is also the *rstwt* keywords to
> define a function of multiple distance restraints, called a "generalized
> distance coordinate" restraint.
> This is the formalism to define the asymmetrical mono-dimensional reaction
> coordinate.
>
> V
>
> On Fri, Oct 19, 2018 at 4:23 PM Zuo, Zhicheng <Zhicheng.Zuo.unthsc.edu>
> wrote:
>
> > Hi, I not not familiar with QM/MM simulation. In your MD.IN file, yet,
> >
> > I noticed that "iat=487,31,31,40" actually corresponds to four atoms.
> >
> > I think you should specify two atoms for distance restraint.
> >
> > Hope it works for you. Good luck!
> >
> >
> > Best
> >
> > Zhicheng Zuo
> >
> > ________________________________
> > From: Vito GENNA <vito.genna.irbbarcelona.org>
> > Sent: Friday, October 19, 2018 6:29:12 AM
> > To: AMBER Mailing List
> > Subject: [AMBER] Constrained QM.MM minimization
> >
> > Dear AMBERusers,
> >
> > I am writing you because I am experiencing a weird behave in my
> > calculations.
> > My goal is to generates the seeds for a subsequent umbrella sampling
> > calculation and to do so, I gonna first reconstruct the potential energy
> > surface with a series of minimized structures.
> >
> > I am using a mono-dimensional and asymmetric reaction coordinate (RC)
> > (widely used for this kind of SN2-type reactions).
> >
> > *Here the input file:*
> > *-----------------------------------------------*
> > PES
> > &cntrl
> > imin=1, maxcyc=500, ntmin=3,
> > ntpr=2, ntb=0, cut=10,
> > ifqnt=1, drms=1E-02,
> > nmropt = 1,
> > &end
> > &qmmm
> > qmmask='.1-50, 468-500, 7643-7648, 9907-9912, 7653-7654, 7669-7670,
> > 8598-8607, 8519-8530, 7681-7692, 76568-76570, 83522-83524',
> > qmcharge=+1,
> > spin=1,
> > qm_theory='EXTERN'
> > qmshake=0,
> > qm_ewald=0,
> > writepdb=1,
> > &end
> > &tc
> > method = 'BLYP',
> > basis = '6-31g*',
> > maxit = 2000,
> > /
> > &wt
> > type='DUMPFREQ', istep1=1,
> > &end
> > &wt
> > type='END',
> > &end
> > DISANG=rst_-1.7
> > DUMPAVE=rst_-1.7.dat
> > LISTIN=POUT
> > LISTOUT=POUT
> > *-----------------------------------------------*
> >
> > here the* rst_-1.7 *file:
> > *-----------------------------------------------*
> > &rst iat=487,31,31,40, r1=-2.2, r2=-1.7, r3=-1.7, r4=-1.2,
> rstwt=-1.0,1.0,
> > rk2=300.0, rk3=300.0, /
> > *-----------------------------------------------*
> > in order to apply an harmonic potential with a well centered on -1.7 (the
> > RC)
> >
> > But, for some mysterious (at least to me) reaons, I got the following RC1
> > values along the calculations:
> >
> > here the* rst_-1.7.dat *file:
> > *-----------------------------------------------*
> > 0 -1.888
> > 1 -1.190
> > 2 -1.802
> > 3 -1.887
> > 4 -1.888
> > 5 -1.888
> > 6 -1.888
> > 7 -1.193
> > *-----------------------------------------------*
> > Of course, fluctuations are expected and wanter in order to reconstruct
> the
> > PMF but I never get a structure in which the RC value is ~-1.7.
> Similarly,
> > for subsequent windows, -1.5, -1.3 and so on...
> >
> > This is the command I run:
> >
> > *sander -O -i min_-1.7.in <http://min_-1.7.in> -o min_-1.7.out -p
> > sys.prmtop -c fixed_-1.9.rst7 -r out_-1.7.rst7*
> >
> > Note that *fixed_-1.9.rst7 *comes from a previous calculations in which
> > -1.9 was the RC1 desired value and that was finely obtained.
> > I am thinking perhaps something is getting wrong with the input file
> > format....possible?
> >
> > Have you got any idea?
> >
> > Thanks in advance
> >
> > Vito
> >
> > PS: terachem1.94, amber14
> >
> > --
> >
> > ***********************************************************************
> > *Vito Genna, Ph.D*
> > *EMBO Fellow*
> >
> > *Postoctoral Researcher*
> >
> > *Molecular Modeling and Bioinformatics*
> > *Orozco Lab*
> >
> > *Institute for Research in Biomedicine (IRB Barcelona)*
> >
> > *Parc Centific de Barcelona*
> >
> > *C/ Baldiri Reixac 10-12*
> > *08028 Barcelona*
> >
> > ***********************************************************************
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> >
> >
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> >
>
>
> --
>
> ***********************************************************************
> *Vito Genna, Ph.D*
> *EMBO Fellow*
>
> *Postoctoral Researcher*
>
> *Molecular Modeling and Bioinformatics*
> *Orozco Lab*
>
> *Institute for Research in Biomedicine (IRB Barcelona)*
>
> *Parc Centific de Barcelona*
>
> *C/ Baldiri Reixac 10-12*
> *08028 Barcelona*
>
> ***********************************************************************
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Fri Oct 19 2018 - 08:30:02 PDT
