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.
