Hi Tim,
Yes the code works pretty well. Btw, still I have to understand why by
default the -r flag of sander writes a restart without box information.
Now I have manually inserted the box dimension at each step.
By augmenting the force to 400 kcal/mol and concomitantly imposing a
slighter stringent convergent criteria, I found my setting.
This is the current -1.7 distribution (not yet converged), which btw looks
much more like a "distribution". At least the first half of a "gaussian"
comes out.
0 -1.888
1 -1.888
2 -1.888
3 -1.888
4 -1.888
5 -1.888
6 -1.888
7 -1.888
8 -1.887
9 -1.886
10 -1.884
11 -1.881
12 -1.871
13 -1.877
14 -1.868
15 -1.854
16 -1.840
17 -1.823
18 -1.805
19 -1.784
20 -1.763
21 -1.744
22 -1.728
23 -1.715
24 -1.707
25 -1.717
26 -1.712
V
On Fri, Oct 19, 2018 at 5:01 PM Timothy Schutt <tschutt7.gmail.com> wrote:
> 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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>
--
***********************************************************************
*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*
***********************************************************************
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Received on Fri Oct 19 2018 - 09:30:03 PDT
