Dear Christoph,
I re-extrapolated ABA angle (table_a1.xvg). The initial distribution
of ABA angle from BI is in Figure 1. After doing "csg_call --options
options.xml --ia-type angle --ia-name angle --sloppy-tables
convert_potential gromacs input output", in the lower angle, the slope is
going down in Figure 2.
Why is this happening?
Thank you.
Best regards,
Changwoon Jang
On Wed, Aug 31, 2016 at 5:21 PM, Christoph Junghans <[email protected]>
wrote:
> 2016-08-31 14:51 GMT-06:00 Chang Woon Jang <[email protected]>:
> > Dear Christoph,
> >
> > It is zero at 180 degree. As you see in the figure (ABAanglehis.png -
> > supposed to be table_a1.xvg), value is zero at 180 degree.
> >
> > What I did, I removed the distribution below 1.5, then it is
> extrapolated.
> > Is this maybe the cause of failure of the run?
> >
> > Do I need to redo csg_call based on this whole distribution instead of
> only
> > 1.5~3.14?
> If it is zero at 180, you should make sure the potential goes to a
> high value there!
>
> Are you trying to do IBI on the bonded interaction, too? Or are they fixed?
>
> Christoph
> >
> > Thank you.
> >
> > Best regards,
> > Changwoon Jang
> >
> >
> > On Wed, Aug 31, 2016 at 4:16 PM, Christoph Junghans <[email protected]>
> > wrote:
> >>
> >> 2016-08-31 12:24 GMT-06:00 Chang Woon Jang <[email protected]>:
> >> > 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).
> >> Are you trying to do IBI on the bonded interaction, too? Or are they
> >> fixed?
> >>
> >> >
> >> > 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.
> >> Does the angle distribution have a non-zero value at 180 degree?
> >>
> >> Christoph
> >> >
> >> > 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]
> >> >> >> >> >
> >> >> >> >> > --
> >> >> >> >> > You received this message because you are subscribed to the
> >> >> >> >> > Google
> >> >> >> >> > Groups
> >> >> >> >> > "votca" group.
> >> >> >> >> > To unsubscribe from this group and stop receiving emails from
> >> >> >> >> > it,
> >> >> >> >> > send
> >> >> >> >> > an
> >> >> >> >> > email to [email protected].
> >> >> >> >> > To post to this group, send email to [email protected].
> >> >> >> >> > Visit this group at https://groups.google.com/group/votca.
> >> >> >> >> > For more options, visit https://groups.google.com/d/optout.
> >> >> >> >>
> >> >> >> >>
> >> >> >> >>
> >> >> >> >> --
> >> >> >> >> Christoph Junghans
> >> >> >> >> Web: http://www.compphys.de
> >> >> >> >>
> >> >> >> >> --
> >> >> >> >> You received this message because you are subscribed to the
> >> >> >> >> Google
> >> >> >> >> Groups
> >> >> >> >> "votca" group.
> >> >> >> >> To unsubscribe from this group and stop receiving emails from
> it,
> >> >> >> >> send
> >> >> >> >> an
> >> >> >> >> email to [email protected].
> >> >> >> >> To post to this group, send email to [email protected].
> >> >> >> >> Visit this group at https://groups.google.com/group/votca.
> >> >> >> >> For more options, visit https://groups.google.com/d/optout.
> >> >> >> >
> >> >> >> >
> >> >> >> >
> >> >> >> > --
> >> >> >> > You received this message because you are subscribed to the
> Google
> >> >> >> > Groups
> >> >> >> > "votca" group.
> >> >> >> > To unsubscribe from this group and stop receiving emails from
> it,
> >> >> >> > send
> >> >> >> > an
> >> >> >> > email to [email protected].
> >> >> >> > To post to this group, send email to [email protected].
> >> >> >> > Visit this group at https://groups.google.com/group/votca.
> >> >> >> > For more options, visit https://groups.google.com/d/optout.
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >> --
> >> >> >> Christoph Junghans
> >> >> >> Web: http://www.compphys.de
> >> >> >>
> >> >> >> --
> >> >> >> You received this message because you are subscribed to the Google
> >> >> >> Groups
> >> >> >> "votca" group.
> >> >> >> To unsubscribe from this group and stop receiving emails from it,
> >> >> >> send
> >> >> >> an
> >> >> >> email to [email protected].
> >> >> >> To post to this group, send email to [email protected].
> >> >> >> Visit this group at https://groups.google.com/group/votca.
> >> >> >> For more options, visit https://groups.google.com/d/optout.
> >> >> >
> >> >> >
> >> >> >
> >> >> >
> >> >> > --
> >> >> > 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]
> >> >> >
> >> >> > --
> >> >> > You received this message because you are subscribed to the Google
> >> >> > Groups
> >> >> > "votca" group.
> >> >> > To unsubscribe from this group and stop receiving emails from it,
> >> >> > send
> >> >> > an
> >> >> > email to [email protected].
> >> >> > To post to this group, send email to [email protected].
> >> >> > Visit this group at https://groups.google.com/group/votca.
> >> >> > For more options, visit https://groups.google.com/d/optout.
> >> >>
> >> >>
> >> >>
> >> >> --
> >> >> Christoph Junghans
> >> >> Web: http://www.compphys.de
> >> >>
> >> >> --
> >> >> You received this message because you are subscribed to the Google
> >> >> Groups
> >> >> "votca" group.
> >> >> To unsubscribe from this group and stop receiving emails from it,
> send
> >> >> an
> >> >> email to [email protected].
> >> >> To post to this group, send email to [email protected].
> >> >> Visit this group at https://groups.google.com/group/votca.
> >> >> For more options, visit https://groups.google.com/d/optout.
> >> >
> >> >
> >> >
> >> >
> >> > --
> >> > 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]
> >> >
> >> > --
> >> > You received this message because you are subscribed to the Google
> >> > Groups
> >> > "votca" group.
> >> > To unsubscribe from this group and stop receiving emails from it, send
> >> > an
> >> > email to [email protected].
> >> > To post to this group, send email to [email protected].
> >> > Visit this group at https://groups.google.com/group/votca.
> >> > For more options, visit https://groups.google.com/d/optout.
> >>
> >>
> >>
> >> --
> >> Christoph Junghans
> >> Web: http://www.compphys.de
> >>
> >> --
> >> You received this message because you are subscribed to the Google
> Groups
> >> "votca" group.
> >> To unsubscribe from this group and stop receiving emails from it, send
> an
> >> email to [email protected].
> >> To post to this group, send email to [email protected].
> >> Visit this group at https://groups.google.com/group/votca.
> >> For more options, visit https://groups.google.com/d/optout.
> >
> >
> >
> >
> > --
> > 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]
> >
> > --
> > You received this message because you are subscribed to the Google Groups
> > "votca" group.
> > To unsubscribe from this group and stop receiving emails from it, send an
> > email to [email protected].
> > To post to this group, send email to [email protected].
> > Visit this group at https://groups.google.com/group/votca.
> > For more options, visit https://groups.google.com/d/optout.
>
>
>
> --
> Christoph Junghans
> Web: http://www.compphys.de
>
> --
> You received this message because you are subscribed to the Google Groups
> "votca" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to [email protected].
> To post to this group, send email to [email protected].
> Visit this group at https://groups.google.com/group/votca.
> For more options, visit https://groups.google.com/d/optout.
>
--
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]
--
You received this message because you are subscribed to the Google Groups
"votca" group.
To unsubscribe from this group and stop receiving emails from it, send an email
to [email protected].
To post to this group, send email to [email protected].
Visit this group at https://groups.google.com/group/votca.
For more options, visit https://groups.google.com/d/optout.
