On Wed, Jun 14, 2023, 22:55 Kankana Bhattacharjee < [email protected]> wrote:
> Sir, now angle_a1.xvg worked for gmx mdrun option. > What did you change? I would like to know, if I run vacuum, single atomistic propane and single > CG propane, all atom propane in vacuum then should I have to use "sd" > integrator in all cases ? > You need some simulation that produces NVT ensemble, so the "sd" integrator is one opinion or you could use "md" and an thermostat. 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&;> > 06/15/23, > 10:21:58 AM > > On Thu, Jun 15, 2023 at 4:32 AM Christoph Junghans <[email protected]> > wrote: > >> >> >> On Wed, Jun 14, 2023, 00:17 Kankana Bhattacharjee < >> [email protected]> wrote: >> >>> Dear Sir, >>> >>> All the table.xvg files (table_b1.xvg, table_b2.xvg, table_a1.xvg) are >>> prepared using csg_call command. Now, I am trying to perform Gromacs CG-MD >>> simulation of single CG propane using GROMACS and executed the >>> command line: >>> >>> 1. >>> >>> gmx_mpi mdrun -v -deffnm cg -tableb table_b1.xvg table_b2.xvg >>> table_a1.xvg >>> >>> >>> >>> *Now, error is coming like this: *In table file 'table_a1.xvg' the x >>> values are not equally spaced: 0.000000 >>> >>> 0.229153 0.343730 >>> >>> How can I fix this issue i.e, equally spacing x values ? >>> >> I am not a 100 percent sure, what is going on! >> Can you post the input files (pot and xvg) for the angle interaction? >> >> 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&;> >>> 06/14/23, >>> 11:46:13 AM >>> >>> On Mon, Jun 12, 2023 at 5:55 PM Christoph Junghans <[email protected]> >>> wrote: >>> >>>> >>>> >>>> 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 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> <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. 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