On Sat, Jun 3, 2023 at 9:00 AM Kankana Bhattacharjee < [email protected]> wrote:
> Thank you sir. But IBI would be for multiple propane molecules. Isn't it ? > It won't be for single propane i think > Yes, IBI (and IMC and RE) are for multiple molecules. > > 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 >> > -- 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/CAHG27e40YztRbF1BeOsaZ9yrZHLWopCvFp41qwaqrPXsn-wcRg%40mail.gmail.com.
