Sir, actually it was given by professor so that, for any arbitrary molecule also I can make itp file to run CG-MD simulation. It is just for my learning purpose.
Suppose, in the tutorial for CG systems topol.top file is there. Like for ibi, imc method etc. topol.top is there. But, for any unknown organic CG molecule how can one generate itp file to run CGMD simulation ? [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&;> 06/03/23, 09:45:05 AM On Sat, Jun 3, 2023 at 9:42 AM Christoph Junghans <[email protected]> wrote: > > > On Fri, Jun 2, 2023 at 21:00 Kankana Bhattacharjee < > [email protected]> wrote: > >> Actually sir, it was asked me to prepare propane.itp (for CG). >> > Sorry, can you explain a bit more why you need an itp file? All the files > (except for the potentials) are in the tutorial already. > >> >> >> >> >> [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&;> >> 06/03/23, >> 08:29:51 AM >> >> On Sat, Jun 3, 2023 at 4:15 AM Christoph Junghans <[email protected]> >> wrote: >> >>> >>> >>> On Fri, Jun 2, 2023 at 12:34 PM Kankana Bhattacharjee < >>> [email protected]> wrote: >>> >>>> >>>> Dear Sir, >>>> >>>> I have done boltzmann inversion of propane. now, for getting nonbonded >>>> parameters what protocol should I follow ? Because, my aim is to generate >>>> GROMACS compatible itp file for CG propane so that, can perform CG-MD using >>>> Votca. >>>> >>> Why can't you use the topology files from the propane tutorial? >>> https://github.com/votca/votca/tree/master/csg-tutorials/propane/ibi >>> I am asking because most of the CG methods VOTCA implement work on >>> tabulated potentials only. >>> >>> Christoph >>> >>> >>>> >>>> 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&;> >>>> 06/03/23, >>>> 12:00:35 AM >>>> >>>> On Fri, Jun 2, 2023 at 9:13 PM Christoph Junghans <[email protected]> >>>> wrote: >>>> >>>>> Forgot to CC the mailing list, so here is the answer for others. >>>>> >>>>> ---------- Forwarded message --------- >>>>> From: Christoph Junghans <[email protected]> >>>>> Date: Fri, Jun 2, 2023 at 8:22 AM >>>>> Subject: Re: [votca] Regarding-Getting-itp-files: >>>>> To: Kankana Bhattacharjee <[email protected]> >>>>> >>>>> >>>>> >>>>> >>>>> On Fri, Jun 2, 2023 at 8:06 AM Kankana Bhattacharjee < >>>>> [email protected]> wrote: >>>>> >>>>>> Sir, after boltzmann inversion, bond.dist.ib, angle.dist.ib and >>>>>> bond.pot.ib, angle.pot.ib (after using tab command)files generated. So, >>>>>> where will I get sigma, epsilon values >>>>>> >>>>> >>>>> I am not a 100% sure what you mean. >>>>> >>>>> When you use nbfunc=1 and comb-rule=1, the sigma and epsilon column in >>>>> the atomtypes block are actually the C6 and C12 parameters (i.e. the >>>>> prefactor of 1/r**6 and 1/r**12). >>>>> But if you then use tables (vdwtype = user in the mdp file), 1/r**6 >>>>> and 1/r**12 gets replaced with the function from files you provided (e.g. >>>>> obtained by boltzmann inversion) And hence in VOTCA we just set C6=C12=1, >>>>> so that the table is used unmodified. >>>>> >>>>> Hope that helps, >>>>> >>>>> 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&;> >>>>>> 06/02/23, >>>>>> 07:34:36 PM >>>>>> >>>>>> On Fri, Jun 2, 2023 at 7:27 PM Christoph Junghans <[email protected]> >>>>>> wrote: >>>>>> >>>>>>> >>>>>>> >>>>>>> On Fri, Jun 2, 2023 at 7:44 AM Kankana Bhattacharjee < >>>>>>> [email protected]> wrote: >>>>>>> >>>>>>>> Sir, I would like to know how sigma, epsilon and default section >>>>>>>> was decided fpr CG-MD simulation ? >>>>>>>> >>>>>>> >>>>>>> no sigma and epsilon, it is all tabulated interactions. >>>>>>> see >>>>>>> >>>>>>> https://github.com/votca/votca/blob/master/csg-tutorials/hexane/ibi_nonbonded/grompp.mdp#L73 >>>>>>> >>>>>>> and those tables you get from boltzmann inversion (or force >>>>>>> matching). >>>>>>> >>>>>>> Christoph >>>>>>> >>>>>>>> ---------- Forwarded message --------- >>>>>>>> From: Christoph Junghans <[email protected]> >>>>>>>> Date: Fri, Jun 2, 2023 at 7:10 PM >>>>>>>> Subject: Re: [votca] Regarding-Getting-itp-files: >>>>>>>> To: Kankana Bhattacharjee <[email protected]> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On Fri, Jun 2, 2023 at 3:40 AM Kankana Bhattacharjee < >>>>>>>> [email protected]> wrote: >>>>>>>> >>>>>>>>> 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 ? >>>>>>>>> >>>>>>>> >>>>>>>> In the topol.top of the coarse grained simulation you can set the >>>>>>>> charge, e.g. see: >>>>>>>> >>>>>>>> https://github.com/votca/votca/blob/master/csg-tutorials/hexane/ibi_nonbonded/topol.top#L5_L8 >>>>>>>> >>>>>>>> >>>>>>>> Christoph >>>>>>>> >>>>>>>> >>>>>>>>> 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 >>>>>>>>>>>> >>>>>>>>>>> >>>>>>>> >>>>>>>> -- >>>>>>>> Christoph Junghans >>>>>>>> Web: http://www.compphys.de >>>>>>>> >>>>>>>> [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, >>>>>>>> 07:13:42 PM >>>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> 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/CAHG27e4fdqGEwaOmCf%2BHbBk%2BQ%3DAyuJ35AGn011ji6CAjdYeAgg%40mail.gmail.com >>>>> <https://groups.google.com/d/msgid/votca/CAHG27e4fdqGEwaOmCf%2BHbBk%2BQ%3DAyuJ35AGn011ji6CAjdYeAgg%40mail.gmail.com?utm_medium=email&utm_source=footer> >>>>> . >>>>> >>>> >>> >>> -- >>> 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/CAMNJFVkMokiQUXYoe2yEUihxgPUPN3vVjvPjO-A9%3DSQtfmyYQw%40mail.gmail.com.
