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/CAMNJFVnLJd7AxztQ%2BFL9o_VUUiPHwCURK_JzRPPP%2BwYbt4ghKw%40mail.gmail.com.
bond.pot.ib
Description: Binary data
bond1.dist.ib
Description: Binary data
bond2.dist.ib
Description: Binary data
<cg_molecule>
<name>ppn</name>
<ident>Protein</ident>
<topology>
<cg_beads>
<cg_bead>
<name>A1</name>
<type>A</type>
<symmetry>1</symmetry>
<mapping>A</mapping>
<beads> 1:ppn:C1 1:ppn:H4 1:ppn:H5 1:ppn:H6 </beads>
</cg_bead>
<cg_bead>
<name>B1</name>
<type>B</type>
<symmetry>1</symmetry>
<mapping>B</mapping>
<beads> 1:ppn:C2 1:ppn:H7 1:ppn:H8 </beads>
</cg_bead>
<cg_bead>
<name>A2</name>
<type>A</type>
<symmetry>1</symmetry>
<mapping>A</mapping>
<beads> 1:ppn:C3 1:ppn:H9 1:ppn:H10 1:ppn:H11 </beads>
</cg_bead>
</cg_beads>
<cg_bonded>
<bond>
<name>bond</name>
<beads>
A1 B1
B1 A2
</beads>
</bond>
<angle>
<name>angle</name>
<beads>
A1 B1 A2
</beads>
</angle>
</cg_bonded>
</topology>
<maps>
<map>
<name>A</name>
<weights> 12 1 1 1 </weights>
</map>
<map>
<name>B</name>
<weights> 12 1 1 </weights>
</map>
</maps>
</cg_molecule>
boltzmann_cmds
Description: Binary data
