On Fri, Jun 30, 2023, 02:36 Kankana Bhattacharjee < [email protected]> wrote:
> > Sir, During mapping using (csg_map) votca one tpr file is needed. But, if > I want to convert an arbitrary AA structure into CG structure then which > tpr file has to be provided? I mean energy minimised ya final npt > production run tor file ? > It doesn't really matter, VOTCA just reads the topology information from the tpr, not positions etc. > On Wed, Jun 28, 2023, 18:47 Christoph Junghans <[email protected]> wrote: > >> >> >> On Tue, Jun 27, 2023 at 9:57 PM Kankana Bhattacharjee < >> [email protected]> wrote: >> >>> Sir, what would be the typical force constant value in case of angle for >>> CG propane if I Don't use tabulated functional form? >>> >> I am not sure out of my head, it has been too long. >> You could make an estimate from Figure 4d of >> http://dx.doi.org/10.1021/ct900369w. >> >> >>> On Tue, Jun 27, 2023, 18:28 Christoph Junghans <[email protected]> >>> wrote: >>> >>>> >>>> >>>> On Tue, Jun 27, 2023, 05:18 Kankana Bhattacharjee < >>>> [email protected]> wrote: >>>> >>>>> Ok. Thank you sir. >>>>> >>>>> Sir, I have got the bond length, angle distribution datas from the >>>>> atomistic simulation using gmx distance and angle options respectively. >>>>> But, how can I invert the bonded potentials i.e, bonded potential plots ? >>>>> Initially, using csg_boltzmann I used the command line: >>>>> >>>>> csg_boltzmann --top topol.tpr --trj traj.trr --cg propane.xml < >>>>> boltzmann_cmds >>>>> From there, I obtained the inverted curve. I would like to fit the >>>>> all atom bonded datas to get the force constant. So, for that I need to >>>>> convert the output file (aa-dist.xvg, aa-angle-dist.xvg). How to do that >>>>> job ? Can it be done using: >>>>> csg_boltzmann --top topol.tpr --trj traj.trr (the trajectory which >>>>> used to get the distribution) --no-map < boltzmann_cmds >>>>> >>>> Sorry, but VOTCA doesn't have a tool to fit force constants! I would >>>> recommend using gnuplot or numpy for that. >>>> >>>> >>>>> >>>>>> On Tue, Jun 27, 2023 at 4:34 PM Christoph Junghans < >>>>> [email protected]> wrote: >>>>> >>>>>> >>>>>> >>>>>> 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: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> * <http://table_linearop.pl>* >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -- Join us on Slack: https://join.slack.com/t/votca/signup --- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/votca/CAHG27e7-OMs4a22-38hy_4_B6p8xcqzKX8K8Jtdzekw1qwpunQ%40mail.gmail.com.
