Thanks.
I would be so thankful if one could comment on below questions;
1. The manual states that the IBI so far only supports iterative refinement
of non-bonded interactions, however, I saw an example of setting.xml file
in mailing list in which the bonded interactions were also defined for
refinement by IBI, so, does IBI also support the bonded interactions?
2. I guess the ensemble chosen for MD simulation during IBI depends on the
physics of the system (similar to the normal MD simulation), however, the
Tcoupl = 0 and Pcoupl = 0 has been assigned for the temperature and
pressure for all of the example of CG I have seen, so, I was wondering if
the ensemble should be similar to the all atoms MD simulation by which
target_rdf.xvg has been calculated, am I right?
3. We have to add the [ defaults ] and [ atomtypes ] section to the
topol.top generated by csg_gmxtopol, if I am not wrong the [ defaults ]
depends on the type of force field we want to use which should be again
similar to the target all atom MD simulation, for the [ atomtypes ], how I
should indicate the C6 and C12 parameter for each bead? of course the C6
and C12 are available in ffnonbonded.itp for individual atoms involved in
each beads but not for the beads itself. For instance to get the mass of
bead we sum up the mass of individual atoms involved in that bead.
4. Below is a part of setting.xml file used in a IBI simulation;
<name>ABA</name>
<min>1.2</min>
<max>2.9</max>
<step>0.001</step>
<inverse>
<!-- target distribution -->
<target>angle1.dist.tgt</target>
<do_potential>0 0 0</do_potential>
<post_update>smooth</post_update>
<post_update_options>
<scale>0.001</scale>
</post_update_options>
<post_add>convergence</post_add>
<gromacs>
<table>table_a1.xvg</table>
</gromacs>
</inverse>
</bonded>
<bonded>
Can you please confirm me that the <target>angle1.dist.tgt</target> is the
one we provide in advance and the <table>table_a1.xvg</table> is the one
which votca results after refinement? (in general for refinement of bonded
and nonbonded interaction <target>case.tgt</target> is the one we provide
and <table>case.table.xvg</table> is the votca give finally)
Also, how I can calculate the "angle1.dist.tgt" one?
How should we know the <min>xx</min> and <max>xxx</max> for each
interaction?
Thank you very much in advance for your time.
Best regards,
Alex
On Wednesday, March 28, 2018 at 3:28:44 AM UTC-4, Christoph Junghans wrote:
>
> On Tue, Mar 27, 2018 at 6:28 PM, Alexander Alexander
> <[email protected] <javascript:>> wrote:
> >
> > Thank Christoph.
> > Actually the xmlwf did not give more information than the parse error in
> the
> > last line.
> >
> > I will take the opportunity to ask one more general question:
> >
> > Using the boltzmann inversion and iterative boltzmann inversion I wand
> to
> > obtain the coarse-grained parameters (bonded and nonbonded) for a
> molecule,
> > the molecule has 53 atom which I have mapped them on 5 beads (3 types)
> and 4
> > bonds and 3 angles. The all atom MD simulation for a system containing
> 307
> > molecules of my interest using gromacs and gromos force filed has also
> been
> > completed.
> > As a new user, I found the votca manual too scattered (sorry for saying
> > that) to follow in order to obtain the CG parameters, I tried to
> understand
> > the examples but still I am not able to fulfill the procedure.
> >
> > By considering the explained molecule I would be so appreciated if one
> could
> > kindly itemize the steps I have to take to obtain all of the CG
> parameters
> > of the molecule of my interest.
> There is no general practice, you will need to check the literature
> and find a system close to what you want to coarse-grain.
> You could trying to coarse-grain all interactions at once, but usually
> something will not work and make the system explode.
> I prefer to start small and build it up, so a.) Boltzmann invert the
> bonded interactions from a single molecule (in vacuum) trajectory,
> then b.) the non-bonded interactions with iterative Boltzmann
> inversion and last you might want to c.) re-iterate the bonded
> interactions.
>
> This has already been extensively discuss on this mailing list, so
> have a look in the archive. The hexane tutorial might be worth looking
> at, too.
>
> Christoph
> >
> > Thank you very much.
> >
> > Best regards,
> > Alex
> >
> >
> >
> >
> > On Tuesday, March 27, 2018 at 4:55:51 PM UTC-4, Christoph Junghans
> wrote:
> >>
> >> On Tue, Mar 27, 2018 at 2:07 PM, Alexander Alexander
> >> <[email protected]> wrote:
> >> >
> >> > Solved now, I was missing a backslash in </ident>.
> >> > Anyway, thank you.
> >> The expat package, provides a little tool called "xmlwf", which allows
> >> you to check whether an xml file is well-formatted.
> >>
> >> Christoph
> >> >
> >> > Regards,
> >> > Alex
> >> >
> >> >
> >> >
> >> > On Tuesday, March 27, 2018 at 2:20:10 PM UTC-4, Alexander Alexander
> >> > wrote:
> >> >>
> >> >>
> >> >> Dear all,
> >> >>
> >> >> The "csg_dump --top case.tpr --cg case.xml" parses error at the last
> >> >> line
> >> >> of my case.xml with the mismatched tag, I can not find out where I
> am
> >> >> doing
> >> >> wrong, so, I would be so appreciated if you could have a look at my
> >> >> attached
> >> >> case.xml,.top,gro files and help me overcome the issue.
> >> >>
> >> >> Thanks
> >> >> Best regards,
> >> >> Alex
> >> >
> >> > --
> >> > You received this message because you are subscribed to the Google
> >> > Groups
> >> > "votca" group.
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> 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
> >
> > --
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>
>
> --
> Christoph Junghans
> Web: http://www.compphys.de
>
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