Dear Christoph,
I have tested IBI with angle potential from hexane tutorial. I replace
hexane angle potential with table_a1.xvg in my system. In topol.top, I used
all tabulated angle potentials (8) instead of harmonic angles (2).
Now, it smoothly works. I think that the A-B-A type angle potential
(table_a1.xvg) has a problem.
As you said, what does that mean of "you might want to extrapolate
toward 180 degree at bit steeper"? I would like to refine the potential of
table_a1.xvg because of the rest of potentials look fine at least IBI
running.
Thank you.
Best regards,
Changwoon Jang
On Wed, Aug 31, 2016 at 1:30 PM, Christoph Junghans <[email protected]>
wrote:
> 2016-08-31 10:58 GMT-06:00 Chang Woon Jang <[email protected]>:
> > Dear Christoph,
> >
> > When I change only harmonic angle from tabulated angle for "TDM"
> > molecule in topology file (topol.top) as follow, it smoothly now works.
> The
> > rest of bond, angle, dihedral still usethe tabulated (8) potentials.
> >
> > What does this mean? Is The tabulated angle potential derived for TDM
> > molecule incorrect?
> I just means something isn't ok with that potential.
> Look at the angle potentials of the original VOTCA paper
> <http://dx.doi.org/10.1021/ct900369w>
> From the tables you sent yesterday, you might want to extrapolate
> toward 180 degree at bit steeper.
>
> If you are doing IBI, you don't have to use the Boltzmann inverted
> potential, you can always start from a harmonic potential as the
> initial guess.
>
>
> Christoph
>
> >
> > [ angles ]
> > 1 3 2 2 1 1.0 <--- originally 8
> > 1 3 4 2 1 1.0 <--- originally 8
> > 1 3 5 2 1 1.0 <--- originally 8
> > 2 3 4 2 1 1.0 <--- originally 8
> > 2 3 5 2 1 1.0 <--- originally 8
> > 4 3 5 2 1 1.0 <--- originally 8
> >
> >
> > Best regards,
> > Changwoon Jang
> >
> >
> >
> > On Wed, Aug 31, 2016 at 11:46 AM, Christoph Junghans <[email protected]
> >
> > wrote:
> >>
> >> 2016-08-31 9:25 GMT-06:00 Chang Woon Jang <[email protected]>:
> >> > Dear Christoph,
> >> >
> >> > IBI still fails few iteration later the angle is going and coming
> at
> >> > the
> >> > boundary. See the figures. I am not sure why GROMACS does not consider
> >> > the
> >> > PBC effect. The 201-202-203 angle looks like over 180 degree. Do you
> >> > have
> >> > any suggestion?
> >> Well, not really. I guess it is time to debug your topology!
> >> I would start with using some harmonic interactions for all angles
> >> (with approximately the right mean and width) and replace them one by
> >> one to see, which one make the simulation crash.
> >>
> >> Christoph
> >> >
> >> > Thank you.
> >> >
> >> > Best regards,
> >> > Changwoon Jang
> >> >
> >> > On Wed, Aug 31, 2016 at 11:05 AM, Christoph Junghans
> >> > <[email protected]>
> >> > wrote:
> >> >>
> >> >> 2016-08-31 8:43 GMT-06:00 Chang Woon Jang <[email protected]>:
> >> >> > Dear Votca Users,
> >> >> >
> >> >> > I have missed the figures. Figure 1 is initial configuration.
> >> >> > Figure
> >> >> > 2 is
> >> >> > the final iteration (1000 iteration) right before the ibi fails.
> >> >> >
> >> >> > Thank you.
> >> >> >
> >> >> > Best regards,
> >> >> > Changwoon Jang
> >> >> >
> >> >> >
> >> >> > On Wed, Aug 31, 2016 at 10:35 AM, Chang Woon Jang
> >> >> > <[email protected]>
> >> >> > wrote:
> >> >> >>
> >> >> >> Dear Votca Users,
> >> >> >>
> >> >> >> I have a question about creating initial configuration of the
> >> >> >> system.
> >> >> >>
> >> >> >> 1. Full atomistic simulation ---- I have run full atomistic
> >> >> >> simulations of polymer system with OPLS-AA force field. Then, it
> >> >> >> (low
> >> >> >> density system) was equilibrated with NVT and NPT simulation for
> 50
> >> >> >> ns.
> >> >> >> Thus, the box under PBC is shrinked from 10nm to about 5nm.
> >> >> >>
> >> >> >> 2. Then, I used the final configuration (confout.gro) in order
> >> >> >> to
> >> >> >> map
> >> >> >> the atomistic system into Coarse-grained system.
> >> >> >>
> >> >> >> I used this CG system for IBI in order to get non-bonded
> >> >> >> potentials.
> >> >> >> However, when I run IBI, I think that some of angle are blowing up
> >> >> >> and
> >> >> >> the
> >> >> >> ibi run finally fail in the beginning. I checked CG trajectory. An
> >> >> >> angle
> >> >> >> seem to be blowing up as shown in figure.
> >> >> >>
> >> >> >> I think this is ok if the system is under PBC. But the error
> >> >> >> message
> >> >> >> keeps indicate this angle has a problem.
> >> >> You might want to run
> >> >> $ gmx trjconv -f conf_in.gro -o conf_out.gro -pbc mol
> >> >> to make molecule whole.
> >> >>
> >> >> Christoph
> >> >> >>
> >> >> >>
> >> >> >> Therefore, I am asking for how you create the initial CG system
> >> >> >> all
> >> >> >> beads are inside box but not at the boundary.
> >> >> >>
> >> >> >> Thank you.
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >> ************************************************************
> ****************************************
> >> >> >> Not all bonded interactions have been properly assigned to the
> >> >> >> domain
> >> >> >> decomposition cells
> >> >> >>
> >> >> >> A list of missing interactions:
> >> >> >> Tab. Angles of 856 missing 1
> >> >> >>
> >> >> >> Molecule type 'TDM'
> >> >> >> the first 10 missing interactions, except for exclusions:
> >> >> >> Tab. Angles atoms 1 3 2 global 201 203
> >> >> >> 202
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >> ************************************************************
> ******************************************
> >> >> >>
> >> >> >> Best regards,
> >> >> >> Changwoon Jang,
> >> >> >>
> >> >> >
> >> >> >
> >> >> >
> >> >> > --
> >> >> > Best regards,
> >> >> > Changwoon Jang,
> >> >> >
> >> >> > Postdoctoral Research Fellow
> >> >> > Department of Chemical & Biological Engineering, Drexel University
> >> >> > 3141 Chestnut Street, Philadelphia, PA 19104
> >> >> >
> >> >> > Voice: (662) 617-2267
> >> >> > E-mail: [email protected]
> >> >> >
> >> >> > --
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> >> >> > an
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> >> >>
> >> >>
> >> >>
> >> >> --
> >> >> Christoph Junghans
> >> >> Web: http://www.compphys.de
> >> >>
> >> >> --
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> >>
> >> --
> >> Christoph Junghans
> >> Web: http://www.compphys.de
> >>
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> >
> >
> >
> >
> > --
> > Best regards,
> > Changwoon Jang,
> >
> > Postdoctoral Research Fellow
> > Department of Chemical & Biological Engineering, Drexel University
> > 3141 Chestnut Street, Philadelphia, PA 19104
> >
> > Voice: (662) 617-2267
> > E-mail: [email protected]
> >
> > --
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>
>
> --
> Christoph Junghans
> Web: http://www.compphys.de
>
> --
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--
Best regards,
Changwoon Jang,
Postdoctoral Research Fellow
Department of Chemical & Biological Engineering, Drexel University
3141 Chestnut Street, Philadelphia, PA 19104
Voice: (662) 617-2267
E-mail: [email protected]
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