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?
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" or "csg_inverse --options settings.xml" 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. 3. For CG simulation the CG configuration should be used or atomistic one? 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 > https://groups.google.com/d/msgid/votca/CAHG27e67gFfpCoCrSE3LqRUd_JJkxhzrX%2BiZjaXqWPZL6KSTXQ%40mail.gmail.com > . > > > > > > > > -- > > 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 > --- > 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/CAHG27e43wNAE%2BD_a4NhA9sCmJT8O8rMd4JpTW-fHrHBU0oOLAg%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/CAAbE4Doyh8wWXaPFoYxHtMPdnrMDA%2BjtBhnPmY3nE9X60asS2g%40mail.gmail.com.
