Dear Sir, I would like to know, how in the case of CG propane.itp file, I have found that, "func type 8" is used which is tabulated functional form. And, in the case of "func type 8", there are two parameters "table number" and "spring constant" values. And, how two parameters (table number, spring constant) are obtained (which is equal to 1 in topol.top file) ? Like, as I am doing it manually, and bonded values obtained from BI method, then how can I mention spring constant, and table number values in bonded.itp file ?
Thanks and 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&;> 06/08/23, 11:08:09 AM On Mon, Jun 5, 2023 at 7:13 PM Kankana Bhattacharjee < [email protected]> wrote: > Ok sir > > On Mon, Jun 5, 2023, 19:00 Christoph Junghans <[email protected]> wrote: > >> >> >> On Mon, Jun 5, 2023 at 7:11 AM Kankana Bhattacharjee < >> [email protected]> wrote: >> >>> Ok sir. >>> If i use CG MD only using gromacs without using votca, is it possible to >>> do with gromacs 2020 or later version? If i don't use iterative methods >>> >> Well even the non-iterative methods like Boltzmann inversion and Force >> Matching use tables. >> You would have to fit them to a Lennard-Jones form to use Gromacs 2020. >> >> Christoph >> >>> >>> On Mon, Jun 5, 2023, 18:16 Christoph Junghans <[email protected]> >>> wrote: >>> >>>> >>>> >>>> On Mon, Jun 5, 2023 at 6:35 AM Kankana Bhattacharjee < >>>> [email protected]> wrote: >>>> >>>>> Ok sir. What should I do to fix it ? >>>>> >>>> Build VOTCA against gromacs-2019. VOTCA even has an option to build its >>>> own gromacs (BUILD_OWN_GROMACS). >>>> >>>> >>>>> Is it true for all iterative methods ? >>>>> >>>> Yes, but of course you can always use lammps to do the 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&;> >>>>> 06/05/23, >>>>> 06:05:14 PM >>>>> >>>>> On Mon, Jun 5, 2023 at 6:04 PM Christoph Junghans <[email protected]> >>>>> wrote: >>>>> >>>>>> >>>>>> >>>>>> On Mon, Jun 5, 2023 at 6:17 AM Kankana Bhattacharjee < >>>>>> [email protected]> wrote: >>>>>> >>>>>>> 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.* >>>>>>> >>>>>> That is right to use tabulated interactions you will to use gromacs >>>>>> 2019 (or lammps). >>>>>> >>>>>> VOTCA also prints a warning about that issue then you build it. >>>>>> Status of tables in newer gromacs versions here: >>>>>> https://gitlab.com/gromacs/gromacs/-/issues/1347, but >>>>>> unfortunately not much has moved. >>>>>> >>>>>> 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&;> >>>>>>> 06/05/23, >>>>>>> 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 >>>>>>>>>> >>>>>>>>> >>>>>> >>>>>> -- >>>>>> 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/CAMNJFVktE%2BKoe0Dj9eNnpXarwmNGre6_n%3Dwi1FN_4rs_O6c0hg%40mail.gmail.com.
