On Mon, Jun 12, 2023, 03:37 Kankana Bhattacharjee < [email protected]> wrote:
> And, sir while using the csg_call command for single propane, then what > settings.xml file has to be used to convert into table.xvg format ? Because > for single propane folder, there is no settings.xml file. > The settings file is just a simple file that contains some more information about the interaction, this file should work: https://github.com/votca/votca/blob/master/csg-tutorials/propane/ibi/settings.xml When you run csg_call it will tell you which items are read. > > > [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&;> > 06/12/23, > 03:03:46 PM > > On Mon, Jun 12, 2023 at 3:00 PM Kankana Bhattacharjee < > [email protected]> wrote: > >> Ok. Thanks a lot sir. But, what would be the maximum value for specifying >> grid in case of bonds ? >> >> >> >> [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&;> >> 06/12/23, >> 02:59:32 PM >> >> On Mon, Jun 12, 2023 at 8:09 AM Christoph Junghans <[email protected]> >> wrote: >> >>> >>> >>> On Fri, Jun 9, 2023 at 5:29 AM Kankana Bhattacharjee < >>> [email protected]> wrote: >>> >>>> Sir, I am not understanding the Resampling and extrapolation steps for >>>> getting bonded.xvg files. For resampling options, in the command line: >>>> csg_resample --in table.pot --out table_resample.pot \ --grid >>>> min:step:max >>>> >>>> How to choose min, step and max values here ? Kindly help me with >>>> this. >>>> >>> There are some conditions that gromacs wants: >>> - bonds type need to start at 0 to max (in nm) >>> - angle type need to from 0 to 180 degrees >>> - dihedrals type need to go from -18o t0 180 degrees >>> (VOTCA internally uses radians, so you will need to convert that) >>> >>> Most of that is implemented in: >>> >>> https://github.com/votca/votca/blob/master/csg/share/scripts/inverse/potential_to_gromacs.sh >>> >>> You can actually try to use that with: >>> $ csg_call --ia-type bond --ia-name bond1 --settings.xml table.xml >>> convert_potential gromacs table.pot table.xvg >>> >>> Also see: https://www.votca.org/csg/preparing.html#exporting-the-table >>> >>> 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&;> >>>> 06/09/23, >>>> 04:58:12 PM >>>> >>>> On Fri, Jun 9, 2023 at 4:05 PM Kankana Bhattacharjee < >>>> [email protected]> wrote: >>>> >>>>> Dear Sir, >>>>> >>>>> When converting the Boltzmann inverted potential (angle.pot.ib) into >>>>> table.xvg using the command line : *csg_call --ia-type angle >>>>> --ia-name angle1 --options table_a1.xml \ convert_potential gromacs >>>>> angle_rad.pot.ib table_a1.xvg* >>>>> then, getting the error like this: >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> *table_linearop.pl <http://table_linearop.pl>: angle_rad.pot.ib to >>>>> angle_rad.pot.scale.3tqbn with x' = 57.2957795*x + 0readin_table: Not >>>>> enought columns in line 1 in file angle_rad.pot.ib, if you don't have >>>>> flags >>>>> in your table add --sloppy-tables option to >>>>> csg_callCallstack:/usr/bin/csg_call - linenumber 199 do_external - >>>>> linenumber 176 in /usr/share/votca/scripts/inverse/functions_common.sh >>>>> /usr/share/votca/scripts/inverse/potential_to_gromacs.sh - linenumber >>>>> 124 do_external - linenumber 22 (see 'csg_call --cat function >>>>> do_external') die - linenumber 2 (see 'csg_call --cat >>>>> function >>>>> die')###################################################################################################################### >>>>> >>>>> ## ERROR: >>>>> >>>>> ## do_external: subscript >>>>> ## >>>>> /usr/share/votca/scripts/inverse/table_linearop.pl >>>>> <http://table_linearop.pl> --on-x angle_rad.pot.ib >>>>> angle_rad.pot.scale.3tqbn 57.2957795 0 ## (from tags table linearop) >>>>> failed >>>>> >>>>> ## Details can be found above >>>>> ## >>>>> >>>>> >>>>> ######################################################################################################################Terminated* >>>>> >>>>> But, for bonded distributions table.xvg files generated. For angle >>>>> potential, not getting the table and not able to figure out the error. >>>>> 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&;> >>>>> 06/09/23, >>>>> 04:02:39 PM >>>>> >>>>> On Fri, Jun 9, 2023 at 3:10 PM Kankana Bhattacharjee < >>>>> [email protected]> wrote: >>>>> >>>>>> Dear Sir, >>>>>> >>>>>> For bonded distribution, if I want to convert the table into xvg >>>>>> format, then for the "Resampling step" the command line is, I want to >>>>>> know >>>>>> what would be the "min:step:max" options for bonded distributions ? I am >>>>>> not understanding this part. >>>>>> >>>>>> csg_resample --in table.pot --out table_resample.pot \ >>>>>> --grid min:step:max >>>>>> >>>>>> I want to know what would be the *"min:step:max"* options for bonded >>>>>> distributions ? I am not understanding this part. >>>>>> >>>>>> >>>>>> 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&;> >>>>>> 06/09/23, >>>>>> 03:08:17 PM >>>>>> >>>>>> On Fri, Jun 9, 2023 at 1:19 PM Kankana Bhattacharjee < >>>>>> [email protected]> wrote: >>>>>> >>>>>>> Sir, for getting the xvg table, at first I directly created >>>>>>> table.xml file for bond length distribution and then used csg_call >>>>>>> command >>>>>>> to convert the table into xvg format. But, I excluded the "Resampling" >>>>>>> and >>>>>>> "Extrapolation" options. Is it the correct path ? >>>>>>> >>>>>>> >>>>>>> >>>>>>> [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&;> >>>>>>> 06/09/23, >>>>>>> 01:14:13 PM >>>>>>> >>>>>>> On Thu, Jun 8, 2023 at 11:07 PM Christoph Junghans < >>>>>>> [email protected]> wrote: >>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> On Thu, Jun 8, 2023 at 07:54 Kankana Bhattacharjee < >>>>>>>> [email protected]> wrote: >>>>>>>> >>>>>>>>> Sir, to convert the bonded potentials into xvg format, at first I >>>>>>>>> have made table_b1.xml for bond1 type and then, used the command line: >>>>>>>>> csg_call --ia-type bond --ia-name bond1 --options table_b1.xml \ >>>>>>>>> convert_potential gromacs angle.pot.ib table_b1.xvg. But, the output >>>>>>>>> file: >>>>>>>>> table_b1.xvg looks somewhat different from the file given in the ibi >>>>>>>>> folder. Kindly provide some suggestions. Sir, my table_b1.xvg is >>>>>>>>> looking >>>>>>>>> somewhat different from that of table_b1.xvg provided in the ibi >>>>>>>>> folder. >>>>>>>>> For converting into table.xvg, should "Resampling", and >>>>>>>>> "Extrapolation" >>>>>>>>> options also have to be followed in case of bonded distributions ? >>>>>>>>> >>>>>>>> It depends on the system, but usually yes! >>>>>>>> >>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> On Thu, Jun 8, 2023 at 6:02 PM Christoph Junghans < >>>>>>>>> [email protected]> wrote: >>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Thu, Jun 8, 2023, 06:29 Kankana Bhattacharjee < >>>>>>>>>> [email protected]> wrote: >>>>>>>>>> >>>>>>>>>>> Sorry sir, bonded section is also there. To obtain a bond table, >>>>>>>>>>> the used command line is: >>>>>>>>>>> >>>>>>>>>>> csg_call --ia-type bond --ia-name XXX --options table.xml \ >>>>>>>>>>> convert_potential gromacs table_extrapolate.pot table.xvg >>>>>>>>>>> >>>>>>>>>>> I would like to know, in --ia-name flag, what I should I put >>>>>>>>>>> there, would it foolow the name which is mentioned in the >>>>>>>>>>> propane.xml file >>>>>>>>>>> in bonded section (bond1, bond2) ? >>>>>>>>>>> >>>>>>>>>> Yes, it is just the same names you defined in table.xml. >>>>>>>>>> >>>>>>>>>> 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&;> >>>>>>>>>>> 06/08/23, >>>>>>>>>>> 03:57:07 PM >>>>>>>>>>> >>>>>>>>>>> On Thu, Jun 8, 2023 at 3:46 PM Kankana Bhattacharjee < >>>>>>>>>>> [email protected]> wrote: >>>>>>>>>>> >>>>>>>>>>>> But, sir for this process, a table.xml file is given for >>>>>>>>>>>> non-bonded intercations. But, how to do the same job for bonded >>>>>>>>>>>> distributions ? >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> [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, >>>>>>>>>>>> 03:44:48 PM >>>>>>>>>>>> >>>>>>>>>>>> On Thu, Jun 8, 2023 at 3:42 PM Christoph Junghans < >>>>>>>>>>>> [email protected]> wrote: >>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> On Thu, Jun 8, 2023, 06:01 Kankana Bhattacharjee < >>>>>>>>>>>>> [email protected]> wrote: >>>>>>>>>>>>> >>>>>>>>>>>>>> Ok. Thank you sir. I understood that, table number concept >>>>>>>>>>>>>> i.e, table_a1.xvg, table_b1.xvg. But, how can one generate those >>>>>>>>>>>>>> files to >>>>>>>>>>>>>> supply in bonded.itp file ? I can see those table (bond1, >>>>>>>>>>>>>> angle1).xvg files >>>>>>>>>>>>>> in the ibi directory. But, how those files get generated ? >>>>>>>>>>>>>> >>>>>>>>>>>>> https://www.votca.org/csg/preparing.html#exporting-the-table >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>>> ---------- Forwarded message --------- >>>>>>>>>>>>>> From: Christoph Junghans <[email protected]> >>>>>>>>>>>>>> Date: Thu, Jun 8, 2023 at 3:27 PM >>>>>>>>>>>>>> Subject: Re: [votca] Regarding-Getting-itp-files: >>>>>>>>>>>>>> To: Kankana Bhattacharjee <[email protected]> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> On Thu, Jun 8, 2023, 01:43 Kankana Bhattacharjee < >>>>>>>>>>>>>> [email protected]> wrote: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> 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 ? >>>>>>>>>>>>>>> >>>>>>>>>>>>>> The spring constant is yet another number the table gets >>>>>>>>>>>>>> multipled with, but for BI you don't need another factor that >>>>>>>>>>>>>> hence we set >>>>>>>>>>>>>> it to 1.0! >>>>>>>>>>>>>> >>>>>>>>>>>>>> The table number is arbitrary, but needs to consistent with >>>>>>>>>>>>>> the files name, table_b<#>.xvg and table_a<#>.xvg. (b for bond, >>>>>>>>>>>>>> a for >>>>>>>>>>>>>> angle, see the Gromacs manual for details). >>>>>>>>>>>>>> >>>>>>>>>>>>>> Christoph >>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> 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&;> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -- 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/CAHG27e7WohuaNePWwAWeYNP8vZygEYjvpj70hXcGC3xR-kh67w%40mail.gmail.com.
