Dear Sir, I would like to know that, in votca beads are defined using "A, B" etc. But, how to understand what type of bead it is i.e, polar, aploar, charged etc. Using A, B beads can anyone run GROMACS MD simulation ?
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, 03:05:36 PM On Fri, Jun 2, 2023 at 11:06 AM Kankana Bhattacharjee < [email protected]> wrote: > 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/CAMNJFVkohPoBQfkQS4uB0VrFZ5kxOqF9j19jsGJO41CZdxUt4w%40mail.gmail.com.
