Thank you sir. But IBI would be for multiple propane molecules. Isn't it ? It won't be for single propane i think
On Sat, Jun 3, 2023, 19:47 Christoph Junghans <[email protected]> wrote: > > > On Sat, Jun 3, 2023 at 3:16 AM Kankana Bhattacharjee < > [email protected]> wrote: > >> Sir, i performed atomistic simulation of single propane in vaccum. But, >> if we use multiple propane simulation in vaccum, then csg_stat can give RDF >> which can be compared with RDF of ibi/imc methods ? >> > The single molecule in vacuum is a common separation strategy to determine > the intertra molecular interactions. In short get the bonded interactions > from BI for the single chain run and then run IBI for the non-bonded > interactions. > see the Tschoep paper from 1998 ( > https://www.votca.org/csg/bibliography.html#tschoep-1998) > > I want to know how to choose which method (ibi, imc) would be accurate to >> give accurate structural properties? >> > That depends on the system. IBI, IMC & Re are all structure-based methods > and try to reproduce the structure. > Usually IBI is more robust, but needs more iterations. But IMC converges > faster, but needs longer iterations. Marvin (who is on the mailing list as > well) wrote an interesting paper about that recently: > https://doi.org/10.1021/acs.jctc.2c00665 > > >> On Sat, Jun 3, 2023, 09:48 Kankana Bhattacharjee < >> [email protected]> wrote: >> >>> 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 >>>> >>> > > -- > 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/CAMNJFVkA1BaRGASCswbGyD%2BEPbaAnP1htyysMb%2B-U2_bwu-9rA%40mail.gmail.com.
