On Mon, Jun 12, 2023, 03:30 Kankana Bhattacharjee < [email protected]> wrote:
> Ok. Thanks a lot sir. But, what would be the maximum value for specifying > grid in case of bonds ? > That is system specific, you have make an educated guess how far the bonds are stretched in the 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&;> > 06/12/23, > 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&;> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 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: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -- 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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