Thanks for the explanation. I have still some difficulty understanding the
process, and I have the following questions:
1. Are C6 and C12 are literally summed up ("+") or they are just combined
during the FM process --- essentially they have not ever gotten separated?
2. Does the FM technique aim to extract a table potential for CG system
from the atomistic system with matching the forces? Can we use this
extracted FM potential table for CG simulations --- not IBI, just normal CG
MD simulation? If so would you please let me know how can I use this
potential table to run CG simulations and what files are needed for that?
Thank you,
Mohsen
On Tue, Jul 20, 2021 at 5:07 PM Christoph Junghans <[email protected]>
wrote:
> On Tue, Jul 20, 2021 at 8:47 AM Mohsen Farshad <[email protected]>
> wrote:
> >
> > Thanks for the explanation. I am a bit confused. Is there any repulsion
> term in the Votca potential? Would you please explain what kind of
> potential is that?
>
> Gromacs just has the C6 and C12 tables columns, but in the case of
> VOTCA we just add the C6 and C12 parts together and you can make one
> of them zero.
> (see
> https://manual.gromacs.org/documentation/2019.5/reference-manual/special/tabulated-interaction-functions.html#user-specified-potential-functions
> )
> Basically because it is not easy to separate the C6 from the C12 part
> and also because you can do some funky things by using the C6 part for
> something else.
>
> >
> > Also in SPCE tutorial, to run CG simulation, it is suggested to use the
> files for ibi example. I have a few questions in regards to this part of
> the tutorial:
> >
> > 1. What command should I use to run coarse grain:
> >
> > "gmx grompp" and then "gmx mdrun -v"
> This runs a MD simulation directly only use that after coarse-graining
> or for atomistic simulation.
>
> >
> > or "csg_inverse --options settings.xml"
> This is the right command to do IBI
>
> >
> > 1. Would you explicitly explain how should I adjust the settings.xml to
> make it compatible with the potential table that comes from FM. The current
> IBI setting.xml uses IBI interactive algorithm. Is that needed to run CG
> simulation using FM potential? --- if setting.xml is not needed please
> ignore this question.
>
> FM is a different CG method than IBI. FM is one shot and done, while
> IBI is iterative.
> You could use the FM potential as a starting potential for IBI, but
> this is kind of pointless as FM matches the forces, while IBI matches
> the structure.
>
> >
> > 3. For CG simulation the CG configuration should be used or atomistic
> one?
> The CG one.
>
> Christoph
>
> >
> > Thank you,
> > Mohsen
> >
> >
> > On Mon, Jul 19, 2021 at 10:38 PM Christoph Junghans <[email protected]>
> wrote:
> >>
> >> On Mon, Jul 19, 2021 at 5:47 PM Mohsen Farshad <
> [email protected]> wrote:
> >> >
> >> > Here are the potential, force, and output potentials. Would you
> please let me know whether they are correct?
> >> The outcomes are actually correct.
> >>
> >> Your forces and the potential ends at 0.9nm and so is the xvg file.
> >> The values smaller than 0.9nm are not zero.
> >> We shift the potential in such a way that it is zero at the cutoff,
> >> hence all values for r> 0.9nm are zero.
> >> We put the values in the C12 column of the gromacs xvg table, hence
> >> columns 2-5 are empty and only columns 6+7 have numbers.
> >>
> >> Christoph
> >> >
> >> > Thank you,
> >> > Mohsen
> >> >
> >> > On Mon, Jul 19, 2021 at 6:34 PM Christoph Junghans <
> [email protected]> wrote:
> >> >>
> >> >> On Mon, Jul 19, 2021 at 3:04 PM Mohsen Farshad <
> [email protected]> wrote:
> >> >> >
> >> >> > Hi Christoph,
> >> >> >
> >> >> > I was able to install the Votca using Spack. However, going
> through the tutorial I confronted an error after executing the following
> command:
> >> >> >
> >> >> > csg_call table integrate CG-CG.force CG-CG.pot
> >> >> >
> >> >> > The last lines of the error is as follows:
> >> >> >
> >> >> > #000:
> /tmp/tuo98996/spack-stage/spack-stage-hdf5-1.10.7-3mcrng3jtezm72xs2i2fbwpwzogxsupf/spack-src/src/H5T.c
> line 1708 in H5Tcopy(): not a datatype or dataset
> >> >> >
> >> >> > major: Invalid arguments to routine
> >> >> >
> >> >> > minor: Inappropriate type
> >> >> >
> >> >> > Running subscript 'table_integrate.pl CG-CG.force CG-CG.pot'
> (from tags table integrate) dir
> /home/tuo98996/spack/opt/spack/linux-centos7-broadwell/gcc-9.3.0/votca-csg-stable-7slgbunnjcw6657pwdjeshozxpfzi3d5/share/votca/scripts/invers
> >> >> >
> >> >> >
> >> >> > The resulting CG table potential is zero for all the distances.
> >> >> The integrate script will only act on the first valid point, usually
> >> >> marked with "i" in the last column of the force table.
> >> >> So that might be the problem. Otherwise send us the force table and
> we
> >> >> can have a look as well.
> >> >>
> >> >> Christoph
> >> >>
> >> >> >
> >> >> >
> >> >> > Looking forward to your feedback,
> >> >> >
> >> >> >
> >> >> > Thanks,
> >> >> >
> >> >> > Mohsen
> >> >> >
> >> >> >
> >> >> >
> >> >> >
> >> >> > On Thu, Jul 15, 2021 at 7:02 PM Christoph Junghans <
> [email protected]> wrote:
> >> >> >>
> >> >> >> Can you run "spack cd -b votca-csg@stable" and look for a .log
> file in there?
> >> >> >>
> >> >> >> Christoph
> >> >> >>
> >> >> >> On Thu, Jul 15, 2021 at 2:42 PM Mohsen Farshad <
> [email protected]> wrote:
> >> >> >> >
> >> >> >> > On the cluster, the run is not ending now. In my own machine,
> it says:
> >> >> >> >
> >> >> >> > ==> Error: votca-csg-stable-t3g3evics7o4vvqtxxunsnx2p67u56bg:
> Package was not installed
> >> >> >> >
> >> >> >> > ==> Error: Installation request failed. Refer to reported
> errors for failing package(s).
> >> >> >> >
> >> >> >> >
> >> >> >> > The last comment on the cluster is following:
> >> >> >> >
> >> >> >> > [+]
> /home/tuo98996/spack/opt/spack/linux-centos7-haswell/gcc-4.8.5/gromacs-2019.6-xtfitykzurvzarvflpj2v6cu3wywr5fc
> >> >> >> >
> >> >> >> >
> >> >> >> >
> >> >> >> > On Thu, Jul 15, 2021 at 4:38 PM Christoph Junghans <
> [email protected]> wrote:
> >> >> >> >>
> >> >> >> >> On Thu, Jul 15, 2021 at 2:34 PM Mohsen Farshad <
> [email protected]> wrote:
> >> >> >> >> >
> >> >> >> >> > Hi Christoph,
> >> >> >> >> >
> >> >> >> >> > After cloning Spack I inserted the following commands on my
> own machine and the cluster, but neither machines were able to successfully
> complete the installation after a relatively long time.
> >> >> >> >> >
> >> >> >> >> > git clone https://github.com/spack/spack.git spack
> >> >> >> >> > source spack/share/spack/setup-env.sh
> >> >> >> >> > spack install votca-csg@stable
> >> >> >> >> >
> >> >> >> >> > Do you think there is something wrong with the compiler or I
> am missing some commands and installation is more complicated than I am
> thinking of?
> >> >> >> >>
> >> >> >> >> Can you post the error message?
> >> >> >> >>
> >> >> >> >> Christoph
> >> >> >> >> >
> >> >> >> >> > I have made sure the Spack is updated.
> >> >> >> >> >
> >> >> >> >> > Looking forward to hearing from you,
> >> >> >> >> >
> >> >> >> >> > Thanks,
> >> >> >> >> > Mohsen
> >> >> >> >> >
> >> >> >> >> > On Sat, Jul 10, 2021 at 10:01 AM Christoph Junghans <
> [email protected]> wrote:
> >> >> >> >> >>
> >> >> >> >> >> On Fri, Jul 9, 2021 at 3:52 PM Christoph Junghans <
> [email protected]> wrote:
> >> >> >> >> >> >
> >> >> >> >> >> > On Fri, Jul 9, 2021 at 3:42 PM Mohsen Farshad <
> [email protected]> wrote:
> >> >> >> >> >> > >
> >> >> >> >> >> > > Hi Votca developers,
> >> >> >> >> >> > >
> >> >> >> >> >> > > Is there a way to solve this issue without the need for
> installation of "votca@stable" using spack?
> >> >> >> >> >> > Not really, we really have to make a 2021.1 release and
> bump the spackage.
> >> >> >> >> >> > Alternatively, you could apply the code change of the
> patch
> >> >> >> >> >> > (
> https://github.com/votca/tools/commit/6bb7e35ba7d1a31247eafb323be2777ec0439cfe
> )
> >> >> >> >> >> > manually.
> >> >> >> >> >> > I also made a quick fix in spack:
> https://github.com/spack/spack/pull/24815
> >> >> >> >> >> > Once that is merged, you should be good to go.
> >> >> >> >> >> The fix is part of spack now, just pull the latest version
> of spack
> >> >> >> >> >> and everything should be fine.
> >> >> >> >> >>
> >> >> >> >> >> >
> >> >> >> >> >> > Christoph
> >> >> >> >> >> >
> >> >> >> >> >> > >
> >> >> >> >> >> > > Thanks,
> >> >> >> >> >> > > Mohsen
> >> >> >> >> >> > > ---------- Forwarded message ---------
> >> >> >> >> >> > > From: [email protected] <Unknown>
> >> >> >> >> >> > > Date: Thursday, July 8, 2021 at 6:09:31 PM UTC-4
> >> >> >> >> >> > > Subject: C++ Compiler issue
> >> >> >> >> >> > > To: [email protected] <Unknown>
> >> >> >> >> >> > >
> >> >> >> >> >> > >
> >> >> >> >> >> > > Hi Votca developers,
> >> >> >> >> >> > >
> >> >> >> >> >> > > My question: C++ Compiler issue: I am trying to install
> VOTCA on a supercomputer using spack. I am getting a C++ error. Could you
> please have a look at the attached log file? I am trying to figure out what
> my next steps are.
> >> >> >> >> >> > >
> >> >> >> >> >> > > Response from Christoph: The issue you found is
> already fixed (see
> >> >> >> >> >> > > https://github.com/votca/tools/pull/361), but not part
> of a release
> >> >> >> >> >> > > yet.
> >> >> >> >> >> > > You can install "votca@stable" using spack to get the
> fix.
> >> >> >> >> >> > >
> >> >> >> >> >> > > Apologies for the test email.
> >> >> >> >> >> > >
> >> >> >> >> >> > > Thank you
> >> >> >> >> >> > > Akash
> >> >> >> >> >> > >
> >> >> >> >> >> > > --
> >> >> >> >> >> > > Join us on Slack: https://join.slack.com/t/votca/signup
> >> >> >> >> >> > > ---
> >> >> >> >> >> > > 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 view this discussion on the web visit
> https://groups.google.com/d/msgid/votca/4ee1f111-852d-4526-9920-55cfe9b110e9n%40googlegroups.com
> .
> >> >> >> >> >> >
> >> >> >> >> >> >
> >> >> >> >> >> >
> >> >> >> >> >> > --
> >> >> >> >> >> > Christoph Junghans
> >> >> >> >> >> > Web: http://www.compphys.de
> >> >> >> >> >>
> >> >> >> >> >>
> >> >> >> >> >>
> >> >> >> >> >> --
> >> >> >> >> >> Christoph Junghans
> >> >> >> >> >> Web: http://www.compphys.de
> >> >> >> >> >>
> >> >> >> >> >> --
> >> >> >> >> >> Join us on Slack: https://join.slack.com/t/votca/signup
> >> >> >> >> >> ---
> >> >> >> >> >> 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 view this discussion on the web visit
> https://groups.google.com/d/msgid/votca/CAHG27e42Gj-VuA2sudLLec34W8J5RNuu0ocod9C8aee7jwoMEg%40mail.gmail.com
> .
> >> >> >> >> >
> >> >> >> >> > --
> >> >> >> >> > Join us on Slack: https://join.slack.com/t/votca/signup
> >> >> >> >> > ---
> >> >> >> >> > 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 view this discussion on the web visit
> https://groups.google.com/d/msgid/votca/CAAbE4DpAJGCt-_E9RLcOQOA8QQ0jDcsm4AyHtHVfGN4JMZiqdA%40mail.gmail.com
> .
> >> >> >> >>
> >> >> >> >>
> >> >> >> >>
> >> >> >> >> --
> >> >> >> >> Christoph Junghans
> >> >> >> >> Web: http://www.compphys.de
> >> >> >> >>
> >> >> >> >> --
> >> >> >> >> Join us on Slack: https://join.slack.com/t/votca/signup
> >> >> >> >> ---
> >> >> >> >> 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 view this discussion on the web visit
> https://groups.google.com/d/msgid/votca/CAHG27e4cEtmjOuKO3QEMgoHsZSyAJ%3Dp5%2BPS2bihs25p6S%3DkZSA%40mail.gmail.com
> .
> >> >> >> >
> >> >> >> > --
> >> >> >> > Join us on Slack: https://join.slack.com/t/votca/signup
> >> >> >> > ---
> >> >> >> > 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 view this discussion on the web visit
> https://groups.google.com/d/msgid/votca/CAAbE4Dq6vsiEjqxsJGoVLawnA4VwPzLaCbO7zn3Avn2xJoa5rg%40mail.gmail.com
> .
> >> >> >>
> >> >> >>
> >> >> >>
> >> >> >> --
> >> >> >> Christoph Junghans
> >> >> >> Web: http://www.compphys.de
> >> >> >>
> >> >> >> --
> >> >> >> Join us on Slack: https://join.slack.com/t/votca/signup
> >> >> >> ---
> >> >> >> 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 view this discussion on the web visit
> https://groups.google.com/d/msgid/votca/CAHG27e6UhCYcqbPEb5tNk7E4dS6-4OZGzmtA9tjc7zUNsAcg2A%40mail.gmail.com
> .
> >> >> >
> >> >> > --
> >> >> > Join us on Slack: https://join.slack.com/t/votca/signup
> >> >> > ---
> >> >> > 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 view this discussion on the web visit
> https://groups.google.com/d/msgid/votca/CAAbE4DqTUn3QnuN1QFwb6UBnouvgbFzAJWfb9YeuL8sPNc7LvQ%40mail.gmail.com
> .
> >> >>
> >> >>
> >> >>
> >> >> --
> >> >> Christoph Junghans
> >> >> Web: http://www.compphys.de
> >> >>
> >> >> --
> >> >> Join us on Slack: https://join.slack.com/t/votca/signup
> >> >> ---
> >> >> 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 view this discussion on the web visit
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> .
> >> >
> >> >
> >> >
> >> > --
> >> > Mohsen Farshad
> >> > Ph.D. Chemistry
> >> > University of Maine
> >> >
> >> > --
> >> > Join us on Slack: https://join.slack.com/t/votca/signup
> >> > ---
> >> > 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 view this discussion on the web visit
> https://groups.google.com/d/msgid/votca/CAAbE4Dr9PXU%3D7j4%3D0TP-azBAHucna2WoWpZxz%3DCGqReCrGnaFA%40mail.gmail.com
> .
> >>
> >>
> >>
> >> --
> >> Christoph Junghans
> >> Web: http://www.compphys.de
> >>
> >> --
> >> Join us on Slack: https://join.slack.com/t/votca/signup
> >> ---
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> Groups "votca" group.
> >> To unsubscribe from this group and stop receiving emails from it, send
> an email to [email protected].
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> .
> >
> > --
> > Join us on Slack: https://join.slack.com/t/votca/signup
> > ---
> > 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 view this discussion on the web visit
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> .
>
>
>
> --
> Christoph Junghans
> Web: http://www.compphys.de
>
> --
> Join us on Slack: https://join.slack.com/t/votca/signup
> ---
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> .
>
--
Mohsen Farshad
Ph.D. Chemistry
University of Maine
--
Join us on Slack: https://join.slack.com/t/votca/signup
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