Dear Sir, This is the Fatal error obtained from inverse.log file:
*Fatal error:The group cutoff scheme has been removed since GROMACS 2020. Please use theVerlet cutoff scheme.* 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, 05:46:29 PM On Mon, Jun 5, 2023 at 5:32 PM Christoph Junghans <[email protected]> wrote: > > > 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/CAMNJFVmgYY2PFDdg-Rk4MOqA%2BWh8TndvPLLnQu8zBXJ5%3DLCKBw%40mail.gmail.com.
