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 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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/CAHG27e5GHcRVQsL7-S%3D4ngJLDT1GR0YgC0TecCtOht1sqea95A%40mail.gmail.com.
