Dear Sir, I am trying to generate the histogram of bonded distribution and convert into the boltzmann inverted potential for single propane which is given in the tutorial. Since, in case of CG propane two bond length is present (A1-B1 and B1-A2) which is mentioned in the propane.xml file and similarly one angle. So, I am not understanding how can I generate distribution of every bond of propane molecule. I have performed short 5 ps run of single propane molecule. When I am adding the line in boltzmann.cmds as: hist bond1.dist.ib *:bond1:* hist bond2.dist.ib *:bond2:*, then no plottable bond1.dist.ib/bond2.dist.ib is generating.
My aim is to generate the every bond length histogram Please provide me the suggestions. Thanks & Regards Kankana Bhattacharjee Ph. D. Scholar Department of Chemistry Ashoka University Sonipat, Haryana [image: Mailtrack] <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&;> Sender notified by Mailtrack <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&;> 06/01/23, 04:51:51 PM On Wed, May 31, 2023 at 10:45 AM Christoph Junghans <[email protected]> wrote: > > > On Tue, May 30, 2023 at 10:46 PM Kankana Bhattacharjee < > [email protected]> wrote: > >> Ok sir. >> >> I have tried to perform boltzmann inversion after short (5 ps) atomistic >> MD run of propane. I am attaching the corresponding grompp.mdp file of the >> atomistic run, distributed bonded potential files, and boltzmann inverted >> bonded potential files. But, not understanding how these potential are >> helping in generating the itp file of CG propane. >> > Well once you have the inverted potentials you can use them in the CG run, > *.pot is the VOTCA format, which you have to convert to xvg (see > https://www.votca.org/csg/preparing.html#exporting-the-table) > > the table_a1 (a1 for Angle 1) and table_b1 (b1 for Bond 1) in the propane > tutorials were generated this way: > https://github.com/votca/votca/tree/master/csg-tutorials/propane/ibi > > And, the thing which I understood is that, boltzmann inversion is used for >> getting all atom inverted potential and force matching is used for getting >> non-bonded potentials. >> > For you can use iterative boltzmann inversion for the non-bonded > interactions. > (Force-matching works for bonded interactions as well, but VOTCA has > implemented that) > > >> >> CG propane itp (topol.top) file is available in ibi/imc methods part of >> votca. Can it be supplied in performing CG-MD simulation using GROMACS ? >> > If you run the propane tutorial after a couple of steps you will have some > tabulated potential that you can use for CG-MD. > > Christoph > >> >> >> >> >> [image: Mailtrack] >> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&;> >> Sender >> notified by >> Mailtrack >> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&;> >> 05/31/23, >> 10:12:10 AM >> >> On Wed, May 31, 2023 at 10:10 AM Christoph Junghans <[email protected]> >> wrote: >> >>> >>> >>> On Tue, May 30, 2023 at 10:33 PM Kankana Bhattacharjee < >>> [email protected]> wrote: >>> >>>> Thank you sir. I would like to know, how can one get gromacs compatible >>>> itp file for a Coarse grained model using votca ? >>>> >>> It is all tabulated interaction, hence no itp files. >>> >>> And the interactions are determined by IBI, IMC or Force Matching, >>> whatever you prefer. >>> >>> Christoph >>> >>>> >>>> >>>> >>>> [image: Mailtrack] >>>> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&;> >>>> Sender >>>> notified by >>>> Mailtrack >>>> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&;> >>>> 05/31/23, >>>> 10:02:22 AM >>>> >>>> On Wed, May 31, 2023 at 9:58 AM Christoph Junghans <[email protected]> >>>> wrote: >>>> >>>>> >>>>> >>>>> On Sun, May 28, 2023 at 10:13 PM Kankana Bhattacharjee < >>>>> [email protected]> wrote: >>>>> >>>>>> Thanks a lot sir for your kind help. >>>>>> >>>>>> I have gone through the topol.top file of spce and propane model >>>>>> using ibi method. I have doubts, how did you define the mass of the >>>>>> beads, >>>>>> charge, bond and angle between beads in topol.top file of the CG model ? >>>>>> >>>>> For a center of mass mapping it is just the sum of the masses (and >>>>> charges), but of course you can do other mappings, too. >>>>> >>>>> In general making a coarse-grained model is more art than science. >>>>> >>>>> Christoph >>>>> >>>>>> >>>>>> >>>>>> >>>>>> [image: Mailtrack] >>>>>> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&;> >>>>>> Sender >>>>>> notified by >>>>>> Mailtrack >>>>>> <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&;> >>>>>> 05/29/23, >>>>>> 09:41:28 AM >>>>>> >>>>>> On Fri, May 26, 2023 at 9:15 PM Christoph Junghans < >>>>>> [email protected]> wrote: >>>>>> >>>>>>> On Thu, May 25, 2023 at 7:23 AM Kankana Bhattacharjee >>>>>>> <[email protected]> wrote: >>>>>>> > >>>>>>> > Dear Sir, >>>>>>> > >>>>>>> > I am learning votca. Now, I have done spce water model atomistic >>>>>>> md run. In the spce/atomistic foolder, grompp.mdp contains integrator as >>>>>>> "sd" . And, I used this settings for short MD run. Then, used csg_tool >>>>>>> to >>>>>>> compute rdf of CG-CG beads and compared with CG-CG with ibi. Then, I >>>>>>> dint >>>>>>> understand the "Running ibi" part of the spce model. It has been asked >>>>>>> to >>>>>>> reduce the number of MD steps in grompp.mdp and adjust the equilibration >>>>>>> time in the settings.xml file. Exactly how to adjust this and why ? I >>>>>>> have >>>>>>> skipped the "Running ibi" option. >>>>>>> >>>>>>> Well, the number of MD steps is in grompp.mdp, while the >>>>>>> equilibration >>>>>>> time is in settings.xml. Longer run will give you smoother RDFs, and >>>>>>> the system usually needs some time to equilibrate from the initial >>>>>>> condition, so you don't want to pick that too short. In the tutorial >>>>>>> we ask folks to explore these options to get some feel for >>>>>>> statistics. >>>>>>> >>>>>>> > >>>>>>> > Second;y, I did force matching part exactly. But, dint understand >>>>>>> exactly what is happening. Like, If I want to generate gromacs >>>>>>> compatible >>>>>>> forcefield.itp for a coarse grained model and perform MD simulation >>>>>>> using >>>>>>> gromacs. THen, how can I generate ttp file for a molecule. >>>>>>> >>>>>>> Force matching return a tabulated force that can then be used to run >>>>>>> the coarse-grained simulation. Have a look at the topol.top of the >>>>>>> spce/ibi example. >>>>>>> >>>>>>> Christoph >>>>>>> >>>>>>> > >>>>>>> > Thanks & Regards >>>>>>> > Kankana Bhattacharjee >>>>>>> > >>>>>>> > -- >>>>>>> > 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/c6eaf8c8-1963-4772-9800-dc9d839dd0bbn%40googlegroups.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/CAHG27e73xWx4bDHzx2AAxA%2B8OaQC%2B_6ru%2B7iACRsRWZrDJOoqQ%40mail.gmail.com >>>>>>> . >>>>>>> >>>>>> >>>>> >>>>> -- >>>>> Christoph Junghans >>>>> Web: http://www.compphys.de >>>>> >>>> >>> >>> -- >>> 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. 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