Thank you very much! I have still a single remaining confusion. Does this mean if I use atomistic configuration and topology files with GC potential table, the system automatically runs coarse-grained simulation using the following commands:
gmx grompp -f grompp.mdp - p topol.top -c conf.gro gmx mdrun -table table_CG_CG.xvg where conf.gro and topol are atomistic configuration and topology files, and table_CG_CG.xvg is the potential table extracted from FM technique. Thanks, Mohsen On Wed, Jul 21, 2021 at 5:09 PM Christoph Junghans <[email protected]> wrote: > On Wed, Jul 21, 2021 at 12:45 PM Mohsen Farshad > <[email protected]> wrote: > > > > Hi Christoph, > > > > Is this correction answer to my question number 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?": > > > > gmx grompp -f grompp.mdp - p topol.top -c confout.gro > > gmx mdrun -table table_CG_CG.xvg > > > > where confout.gro is GC configuration file, and table_CG_CG.xvg is the > potential table extracted from FM technique. > Yes that that is correct, but can also use the mapped atomistic > conf.gro instead of confout.gro > > Christoph > > > > Thanks, > > Mohsen > > > > On Wed, Jul 21, 2021 at 11:56 AM Mohsen Farshad < > [email protected]> wrote: > >> > >> 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 > 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 > . > >>> > >>> > >>> > >>> -- > >>> 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/CAHG27e5X1WAuY55LbM3_o5JP2ubHRgJexuHoO0_89bn2YcXvzw%40mail.gmail.com > . > >> > >> > >> > >> -- > >> Mohsen Farshad > >> Ph.D. Chemistry > >> University of Maine > > > > > > > > -- > > 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/CAAbE4DpT89%2BR7m3%3DoFnT_JiEtV6Kx%3DuNSqohEZ5AW8bEBiFygg%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/CAHG27e6UmuWsd0XJ0NBE6McMTgsYPArPRDNo5OySir-jpAJNYQ%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/CAAbE4DpX7MN5NOxQC5SBbQfKESFyVt0iL_jb0sD4%3DVb3%2BMh%2B6w%40mail.gmail.com.
