Dear Sir, I have included the individual bond section in propane.xml file. Now, distribution is generating. But, for getting non-bonded parameters, which procedure should I have to follow ? I can use either Force Matching or Iterative methods to get non-bonded parameters.
[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&;> 06/02/23, 11:03:20 AM On Fri, Jun 2, 2023 at 9:49 AM Kankana Bhattacharjee < [email protected]> wrote: > Dear Sir, > > I used this command line for bonded distribution: > > csg_boltzmann --top topol.tpr --trj traj.trr --cg propane.xml < > boltzmann_cmds > > After that, got average bond length and angle distribution. And, bond > section is already present in my propane.xml file. But, still dint get any > plottable bond1.dist.ib and bond2.dist.ib files. > I am attaching the files here. > Please kindly help me > > Thanks & Regards > Kankana Bhattacharjee > > > > [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&;> > 06/02/23, > 09:37:49 AM > > On Fri, Jun 2, 2023 at 7:26 AM Christoph Junghans <[email protected]> > wrote: > >> >> >> On Thu, Jun 1, 2023 at 5:22 AM Kankana Bhattacharjee < >> [email protected]> wrote: >> >>> 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. >>> >>> If you don't want to average over the 2 bonds the easiest way to do that >> is to add another bond block here: >> >> https://github.com/votca/votca/blob/master/csg-tutorials/propane/atomistic/propane.xml#L34_L40 >> >> the names should be "bond1" and "bond2" for your application above. >> >> And then run csg_stat (or csg_boltzmann): >> >> https://github.com/votca/votca/blob/master/csg-tutorials/propane/atomistic/run.sh#L22 >> >> Christoph >> >> There is >> >>> 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 >>>> >>> >> >> -- >> 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/CAMNJFV%3Dn0BmOB9drEyqd%2Bhdm9v6wcxYRXYVc8DM0imDzRqNLEQ%40mail.gmail.com.
