On Tue, Jun 27, 2023, 04:13 Kankana Bhattacharjee < [email protected]> wrote:
> > Sir, I want to convert an atomistic structure into CG by providing the > mapping file but for specific molecule I want to ignore the mapping. How to > do that using csg_map tool ? As csg_map is having only --no-map option ? > How can I ignore the mapping for specific molecule during the conversion > process using csg_map tool ? > There is a --map-ignore option. See https://www.votca.org/csg/reference.html#csg-map > Your suggestions would be much appreciated. > > > > [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&;> > 06/27/23, > 03:39:45 PM > > On Wed, Jun 21, 2023 at 8:48 PM Christoph Junghans <[email protected]> > wrote: > >> >> >> On Wed, Jun 21, 2023 at 7:21 AM Kankana Bhattacharjee < >> [email protected]> wrote: >> >>> Sir, I have attached the ppt where bond length distribution of AA and CG >>> run is attached. I used gmx distance to plot the distance distribution. >>> >> Looks like your system gets stuck around 0.075nm, what is the minimum of >> your IB potential for the bond? >> >> Christoph >> >>> >>> On Wed, Jun 21, 2023 at 6:36 PM Christoph Junghans <[email protected]> >>> wrote: >>> >>>> >>>> >>>> On Tue, Jun 20, 2023 at 9:57 PM Kankana Bhattacharjee < >>>> [email protected]> wrote: >>>> >>>>> Sir, I am not getting the same atomistic bonded distribution in case >>>>> of CG run of propane. I used the atomistic grompp.mdp file for the CG >>>>> propane vacuum simulation. Kindly suggest me what should I do to fix this >>>>> ? >>>>> >>>> I don't think the parameters in the mdp file play a bit role as long as >>>> as you sample the same ensemble (NVT) and density (molecules per box). How >>>> different are the distributions? For non-iterative Boltzmann inversion, it >>>> will never match a 100%, hence most folks do iterative boltzmann inversion. >>>> >>>> Christoph >>>> >>>>> >>>>> On Tue, Jun 20, 2023 at 6:48 PM Kankana Bhattacharjee < >>>>> [email protected]> wrote: >>>>> >>>>>> Yes sir. >>>>>> >>>>>> On Tue, Jun 20, 2023 at 6:44 PM Christoph Junghans < >>>>>> [email protected]> wrote: >>>>>> >>>>>>> >>>>>>> >>>>>>> On Tue, Jun 20, 2023 at 4:07 AM Kankana Bhattacharjee < >>>>>>> [email protected]> wrote: >>>>>>> >>>>>>>> Sir, I ran the CGMD simulation using gromacs by providing the >>>>>>>> grompp.mdp file of the atomistic run. I was not sure about that. In >>>>>>>> Votca >>>>>>>> CG methods, grompp.mdp are different in both ibi and imc methods. And, >>>>>>>> the >>>>>>>> bonded distributions of the CGMD run is not matching with the AA run at >>>>>>>> all. I would like to know, which grompp.mdp file has to be provided >>>>>>>> for the >>>>>>>> CGMD run using gromacs (I mean ibi ya imc one) ? >>>>>>>> >>>>>>> You mean this one: >>>>>>> >>>>>>> https://github.com/votca/votca/blob/master/csg-tutorials/propane/ibi/grompp.mdp >>>>>>> >>>>>>> >>>>>>>> On Mon, Jun 19, 2023 at 11:46 PM Kankana Bhattacharjee < >>>>>>>> [email protected]> wrote: >>>>>>>> >>>>>>>>> Thanks Sir >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>> [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&;> >>>>>>>>> 06/19/23, >>>>>>>>> 11:46:02 PM >>>>>>>>> >>>>>>>>> On Mon, Jun 19, 2023 at 9:02 PM Christoph Junghans < >>>>>>>>> [email protected]> wrote: >>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> On Mon, Jun 19, 2023 at 5:25 AM Kankana Bhattacharjee < >>>>>>>>>> [email protected]> wrote: >>>>>>>>>> >>>>>>>>>>> Sir, I am using gmx angle and gmx distance for computing bond >>>>>>>>>>> length and angle distributions from the AA and CGMD runs. For doing >>>>>>>>>>> angle >>>>>>>>>>> distributions from AA run, at first converted the atomistic >>>>>>>>>>> trajectory into >>>>>>>>>>> CG trajectory (traj-mapped trajectory). >>>>>>>>>>> Ist command line: >>>>>>>>>>> >>>>>>>>>>> csg_map --top topol.tpr --trj traj-10ns.trr --cg propane.xml >>>>>>>>>>> --out traj-mapped.xtc >>>>>>>>>>> Then, made the index file for angle distribution as: (index file >>>>>>>>>>> making is same in both AA and CGMD runs) >>>>>>>>>>> [ angles ] >>>>>>>>>>> 1 2 3 for both aa and cgmd runs. >>>>>>>>>>> Then, used the command line in gromacs : >>>>>>>>>>> >>>>>>>>>>> gmx angle -f traj-mapped.xtc -n aa-angle1.ndx -od >>>>>>>>>>> aa-angle-dist.xvg >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> But, I am not understanding how to do bond length distribution >>>>>>>>>>> in both AA and CGMD runs. I mean, how to make the index file for >>>>>>>>>>> bond >>>>>>>>>>> length distribution in both AA and CGMD runs. Using gmx distance I >>>>>>>>>>> am >>>>>>>>>>> trying to do this job. But, not understanding how to make index >>>>>>>>>>> file for >>>>>>>>>>> the same. >>>>>>>>>>> >>>>>>>>>> Sorry this is more a question for the gromacs mailing list. >>>>>>>>>> >>>>>>>>>> Christoph >>>>>>>>>> >>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> Kindly help me with this. >>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> On Mon, Jun 19, 2023 at 10:46 AM Kankana Bhattacharjee < >>>>>>>>>>> [email protected]> wrote: >>>>>>>>>>> >>>>>>>>>>>> Also sir, I am having one doubt, previously I obtained bond, >>>>>>>>>>>> angle distributions using csg_boltzmann tool from the atomistic >>>>>>>>>>>> run and >>>>>>>>>>>> now, should I have to only use CG trajectory for comparing the >>>>>>>>>>>> distributions i.e, using only csg_stat tool. >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> >>>>>>>>>>>> [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&;> >>>>>>>>>>>> 06/19/23, >>>>>>>>>>>> 10:44:34 AM >>>>>>>>>>>> >>>>>>>>>>>> On Mon, Jun 19, 2023 at 10:37 AM Kankana Bhattacharjee < >>>>>>>>>>>> [email protected]> wrote: >>>>>>>>>>>> >>>>>>>>>>>>> But sir, after executing the command line: >>>>>>>>>>>>> csg_stat --top topol.tpr --trj traj-mapped.xtc --cg >>>>>>>>>>>>> propane.xml --options settings.xml >>>>>>>>>>>>> *Error is: * >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> *an error occurred:settings.xml: Parse error at line 35no >>>>>>>>>>>>> element found: iostream error* >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> *I am not able to figure out the error. Also, in case of >>>>>>>>>>>>> propane 2 bond is present, should I have to include 2 bonds in >>>>>>>>>>>>> the settings >>>>>>>>>>>>> file for getting average bond distributions from the atomistic >>>>>>>>>>>>> run. I am >>>>>>>>>>>>> attaching the settings.xml file here. Kindly help me with this. * >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>>>> [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&;> >>>>>>>>>>>>> 06/19/23, >>>>>>>>>>>>> 10:34:54 AM >>>>>>>>>>>>> >>>>>>>>>>>>> On Mon, Jun 19, 2023 at 10:31 AM Christoph Junghans < >>>>>>>>>>>>> [email protected]> wrote: >>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>> On Sun, Jun 18, 2023 at 10:04 PM Kankana Bhattacharjee < >>>>>>>>>>>>>> [email protected]> wrote: >>>>>>>>>>>>>> >>>>>>>>>>>>>>> Sir, for AA simulation, options would be like this : >>>>>>>>>>>>>>> csg_stat --top topol.tpr --trj traj-mapped.xtc --cg >>>>>>>>>>>>>>> propane.xml (normal mapping fie) --options settings.xml >>>>>>>>>>>>>>> >>>>>>>>>>>>>> With a mapping file, you want to use the original (AA / >>>>>>>>>>>>>> not-mapped) trajectory. >>>>>>>>>>>>>> You can decide 1) use csg_stat on AA traj with a mapping >>>>>>>>>>>>>> file, or 2) map the traj first and then use the same command as >>>>>>>>>>>>>> for the CG >>>>>>>>>>>>>> runs. >>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> And, for CGMD run, >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> csg_stat --top topol.tpr (CG one) --trj CG.xtc --cg 1to 1 >>>>>>>>>>>>>>> mapping.xml --options settings.xml >>>>>>>>>>>>>>> >>>>>>>>>>>>>> that is right! >>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> Is it correct sir ? >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> [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&;> >>>>>>>>>>>>>>> 06/19/23, >>>>>>>>>>>>>>> 09:31:40 AM >>>>>>>>>>>>>>> >>>>>>>>>>>>>>> On Sat, Jun 17, 2023 at 8:44 PM Kankana Bhattacharjee < >>>>>>>>>>>>>>> [email protected]> wrote: >>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> Ok. Thank you sir >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> On Sat, Jun 17, 2023, 20:32 Christoph Junghans < >>>>>>>>>>>>>>>> [email protected]> wrote: >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> On Sat, Jun 17, 2023 at 8:47 AM Kankana Bhattacharjee < >>>>>>>>>>>>>>>>> [email protected]> wrote: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> Sir, i performed single atomistic and XG trajectory. Now >>>>>>>>>>>>>>>>>> i want to compare bonded distributions in both runs. Using >>>>>>>>>>>>>>>>>> csg_boltzmann i >>>>>>>>>>>>>>>>>> obtained bond.dist.ib and angle.dist.in plot. Now, >>>>>>>>>>>>>>>>>> should I have to compare this with CG run using >>>>>>>>>>>>>>>>>> csg_boltzmann tool by >>>>>>>>>>>>>>>>>> providing 1to 1 mapping file of propane and settings file ? >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> csg_boltzmann doesn't need a 1:1 mapping, that is only >>>>>>>>>>>>>>>>> needed when using csg_stat. >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> If i use csg_stat then, which settings file I have to use >>>>>>>>>>>>>>>>>> ? >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> You need a settings file that contains the information >>>>>>>>>>>>>>>>> about the bonded interactions. As I said earlier the propane >>>>>>>>>>>>>>>>> tutorials >>>>>>>>>>>>>>>>> doesn't have that, but you can adopt the file from the hexane >>>>>>>>>>>>>>>>> tutorial, see: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> https://github.com/votca/votca/tree/master/csg-tutorials/hexane/ibi_all >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> Because there is one settings file in propane/atomistic >>>>>>>>>>>>>>>>>> directory containing nonbonded information only. How bonded >>>>>>>>>>>>>>>>>> distributions i >>>>>>>>>>>>>>>>>> have to include there. Kindly help me with this. >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> As I said earlier, just add a block like this: >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> https://github.com/votca/votca/blob/master/csg-tutorials/hexane/ibi_all/settings.xml#L4_L15 >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> On Sat, Jun 17, 2023, 19:50 Christoph Junghans < >>>>>>>>>>>>>>>>>> [email protected]> wrote: >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> On Sat, Jun 17, 2023 at 1:23 AM Kankana Bhattacharjee < >>>>>>>>>>>>>>>>>>> [email protected]> wrote: >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> Sir, from single propane (atomistic) run, I obtained >>>>>>>>>>>>>>>>>>>> bonded distributions as (bond1.dist.ib, bond2.dist.ib and >>>>>>>>>>>>>>>>>>>> angle.dist.ib) >>>>>>>>>>>>>>>>>>>> using csg_boltzmann tool. Should I have to compare these >>>>>>>>>>>>>>>>>>>> distributions >>>>>>>>>>>>>>>>>>>> with Coarse grained MD simulations ? I am not >>>>>>>>>>>>>>>>>>>> understanding how to compare >>>>>>>>>>>>>>>>>>>> for bonded distributions with Coarse grained runs ? >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> I am not sure what you are trying to achieve but for a >>>>>>>>>>>>>>>>>>> structure-based CG model you want the AA and CG >>>>>>>>>>>>>>>>>>> distributions to look the >>>>>>>>>>>>>>>>>>> same, hence you want to compare them. >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> [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&;> >>>>>>>>>>>>>>>>>>>> 06/17/23, >>>>>>>>>>>>>>>>>>>> 12:50:14 PM >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> On Sat, Jun 17, 2023 at 8:58 AM Kankana Bhattacharjee < >>>>>>>>>>>>>>>>>>>> [email protected]> wrote: >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> Thanks a lot sir. I would like to get the bonded >>>>>>>>>>>>>>>>>>>>> distributions from csg_stat tool. And, I want to average >>>>>>>>>>>>>>>>>>>>> the bond lengths. >>>>>>>>>>>>>>>>>>>>> dont want nonbonded distributions. So, what would be the >>>>>>>>>>>>>>>>>>>>> format of settings >>>>>>>>>>>>>>>>>>>>> file to include the bond part so that, I can get average >>>>>>>>>>>>>>>>>>>>> bond length >>>>>>>>>>>>>>>>>>>>> distribution. >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> [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&;> >>>>>>>>>>>>>>>>>>>>> 06/17/23, >>>>>>>>>>>>>>>>>>>>> 08:54:09 AM >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> On Sat, Jun 17, 2023 at 12:53 AM Christoph Junghans < >>>>>>>>>>>>>>>>>>>>> [email protected]> wrote: >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> PS: gromacs has a tool to calculate bond lengths as >>>>>>>>>>>>>>>>>>>>>> well. >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>> On Fri, Jun 16, 2023 at 13:22 Christoph Junghans < >>>>>>>>>>>>>>>>>>>>>> [email protected]> wrote: >>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> On Fri, Jun 16, 2023 at 10:35 Kankana Bhattacharjee < >>>>>>>>>>>>>>>>>>>>>>> [email protected]> wrote: >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> Thank you sir. I would like to know, why 1 to 1 >>>>>>>>>>>>>>>>>>>>>>>> mapping scheme is used ? >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> You need the mapping file to define the bonds, not >>>>>>>>>>>>>>>>>>>>>>> all topology files had that information hence votca >>>>>>>>>>>>>>>>>>>>>>> reads it from the >>>>>>>>>>>>>>>>>>>>>>> mapping file. >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> And, for getting bonded distribution (bond length 1, >>>>>>>>>>>>>>>>>>>>>>>> bond length 2) from AA run, how settings.xml file >>>>>>>>>>>>>>>>>>>>>>>> would be helpful as that >>>>>>>>>>>>>>>>>>>>>>>> file is having nonbonded interaction terms. >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> If you don’t want to average over the bonds you will >>>>>>>>>>>>>>>>>>>>>>> have to list bond1 and bond2 separately in the settings >>>>>>>>>>>>>>>>>>>>>>> and mapping file. >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> If you don’t need the non-bonded distributions just >>>>>>>>>>>>>>>>>>>>>>> drop these sections from the file. >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> I would like to visualise bond length and angle >>>>>>>>>>>>>>>>>>>>>>>> distribution. >>>>>>>>>>>>>>>>>>>>>>>> In case of CG run, what would be the options ? >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> pick your favorite tool, matplotlib or gnuplot is >>>>>>>>>>>>>>>>>>>>>>> what most people are using! >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>> Christoph >>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> On Fri, Jun 16, 2023, 21:09 Christoph Junghans < >>>>>>>>>>>>>>>>>>>>>>>> [email protected]> wrote: >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> On Fri, Jun 16, 2023 at 8:32 AM Kankana >>>>>>>>>>>>>>>>>>>>>>>>> Bhattacharjee <[email protected]> >>>>>>>>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Thank you sir for your kind help. >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> I converted atomistic trajectory into CG >>>>>>>>>>>>>>>>>>>>>>>>>> trajectory using csg_map tool. And, I have CG >>>>>>>>>>>>>>>>>>>>>>>>>> trajectory from CGMD run. >>>>>>>>>>>>>>>>>>>>>>>>>> So, if I use csg_stat tool, then what should be the >>>>>>>>>>>>>>>>>>>>>>>>>> exact command line >>>>>>>>>>>>>>>>>>>>>>>>>> option for each atomistic and CG runs: >>>>>>>>>>>>>>>>>>>>>>>>>> If I want to calculate bonded distribution for AA >>>>>>>>>>>>>>>>>>>>>>>>>> run: then, csg_stat --trj traj-mapped.xtc (atomistic >>>>>>>>>>>>>>>>>>>>>>>>>> trajectory mapped into >>>>>>>>>>>>>>>>>>>>>>>>>> CG) then, what would be the other options for >>>>>>>>>>>>>>>>>>>>>>>>>> getting bond length, angle >>>>>>>>>>>>>>>>>>>>>>>>>> distribution and the same thing for CGMD run. >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> csg_stat --top topol.tpr --trj traj-mapped.xtc >>>>>>>>>>>>>>>>>>>>>>>>> --options settings.xml --cg 1to1map.xml. >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Here is an example for 1to1 map for hexane: >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/votca/votca/blob/master/csg-tutorials/hexane/ibi_all/hexane_cg.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&;> >>>>>>>>>>>>>>>>>>>>>>>>>> 06/16/23, >>>>>>>>>>>>>>>>>>>>>>>>>> 07:51:54 PM >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> On Fri, Jun 16, 2023 at 6:29 PM Christoph >>>>>>>>>>>>>>>>>>>>>>>>>> Junghans <[email protected]> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> On Fri, Jun 16, 2023, 06:07 Kankana >>>>>>>>>>>>>>>>>>>>>>>>>>> Bhattacharjee <[email protected]> >>>>>>>>>>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Ok. Thank you sir. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> I would like to compare the bonded >>>>>>>>>>>>>>>>>>>>>>>>>>>> distributions from AA and CG simulation. I have >>>>>>>>>>>>>>>>>>>>>>>>>>>> performed simulation using >>>>>>>>>>>>>>>>>>>>>>>>>>>> GROMACS software. How can I do this job ? >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> You could run csg_stat on both trajectories. Use >>>>>>>>>>>>>>>>>>>>>>>>>>> a 1:1 mapping file for the CG case and a normal >>>>>>>>>>>>>>>>>>>>>>>>>>> mapping file for the AA >>>>>>>>>>>>>>>>>>>>>>>>>>> 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&;> >>>>>>>>>>>>>>>>>>>>>>>>>>>> 06/16/23, >>>>>>>>>>>>>>>>>>>>>>>>>>>> 05:34:12 PM >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Jun 15, 2023 at 5:54 PM Christoph >>>>>>>>>>>>>>>>>>>>>>>>>>>> Junghans <[email protected]> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> 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 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> <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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