On Sun, Jun 4, 2023, 23:15 Kankana Bhattacharjee < [email protected]> wrote:
> Dear Sir, > > RDF for A-A, B-B, A-B computed from atomistic simulation using csg_stat > tool. Now, I am doing ibi method. But, error is coming during step 1 like > this: > Appending to existing logfile inverse.log > We are doing Method: ibi > step 0 is already done - skipping > Doing iteration 1 (dir step_001) > Simulation with gromacs > Automatically added 'cutoff-scheme = Group' to grompp.mdp, tabulated > interactions only work with Group cutoff-scheme! > > ################################################################################################################## > # > # > # ERROR: > # > # critical: 'gmx grompp -n index.ndx -f grompp.mdp -p topol.top -o > topol.tpr -c conf.gro' failed # > # For details see the logfile > /mnt/c/Users/KANKANA/Downloads/votca/csg-tutorials/propane/ibi-kankana/inverse.log > # > Please look up and post the detailed error message from inverse.log. # > # > > ################################################################################################################## > Terminated > > Kindly help me with this. > > 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&;> > 06/05/23, > 10:44:51 AM > > On Sat, Jun 3, 2023 at 8:42 PM Christoph Junghans <[email protected]> > wrote: > >> >> >> 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/CAHG27e4SgCERsPRWZieDAhB8%2BfuXX_eoen6RnFWVeoK8MTM-Qg%40mail.gmail.com.
