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: >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> csg_boltzmann --top topol.tpr --trj traj.trr --cg >>>>>>>>>>>>>>>>>>>>>>>> propane.xml < boltzmann_cmds >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> After that, got average bond length and angle >>>>>>>>>>>>>>>>>>>>>>>> distribution. And, bond section is already present in >>>>>>>>>>>>>>>>>>>>>>>> my propane.xml file. >>>>>>>>>>>>>>>>>>>>>>>> But, still dint get any plottable bond1.dist.ib and >>>>>>>>>>>>>>>>>>>>>>>> bond2.dist.ib files. >>>>>>>>>>>>>>>>>>>>>>>> I am attaching the files here. >>>>>>>>>>>>>>>>>>>>>>>> Please kindly help me >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> 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, >>>>>>>>>>>>>>>>>>>>>>>> 09:37:49 AM >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> On Fri, Jun 2, 2023 at 7:26 AM Christoph Junghans < >>>>>>>>>>>>>>>>>>>>>>>> [email protected]> wrote: >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> On Thu, Jun 1, 2023 at 5:22 AM Kankana >>>>>>>>>>>>>>>>>>>>>>>>> Bhattacharjee <[email protected]> >>>>>>>>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Dear Sir, >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> I am trying to generate the histogram of bonded >>>>>>>>>>>>>>>>>>>>>>>>>> distribution and convert into the boltzmann inverted >>>>>>>>>>>>>>>>>>>>>>>>>> potential for single >>>>>>>>>>>>>>>>>>>>>>>>>> propane which is given in the tutorial. Since, in >>>>>>>>>>>>>>>>>>>>>>>>>> case of CG propane two >>>>>>>>>>>>>>>>>>>>>>>>>> bond length is present (A1-B1 and B1-A2) which is >>>>>>>>>>>>>>>>>>>>>>>>>> mentioned in the >>>>>>>>>>>>>>>>>>>>>>>>>> propane.xml file and similarly one angle. So, I am >>>>>>>>>>>>>>>>>>>>>>>>>> not understanding how >>>>>>>>>>>>>>>>>>>>>>>>>> can I generate distribution of every bond of propane >>>>>>>>>>>>>>>>>>>>>>>>>> molecule. I have >>>>>>>>>>>>>>>>>>>>>>>>>> performed short 5 ps run of single propane molecule. >>>>>>>>>>>>>>>>>>>>>>>>>> When I am adding the >>>>>>>>>>>>>>>>>>>>>>>>>> line in boltzmann.cmds as: >>>>>>>>>>>>>>>>>>>>>>>>>> hist bond1.dist.ib *:bond1:* >>>>>>>>>>>>>>>>>>>>>>>>>> hist bond2.dist.ib *:bond2:*, then no plottable >>>>>>>>>>>>>>>>>>>>>>>>>> bond1.dist.ib/bond2.dist.ib is generating. >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> If you don't want to average over the 2 bonds the >>>>>>>>>>>>>>>>>>>>>>>>> easiest way to do that is to add another bond block >>>>>>>>>>>>>>>>>>>>>>>>> here: >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/votca/votca/blob/master/csg-tutorials/propane/atomistic/propane.xml#L34_L40 >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> the names should be "bond1" and "bond2" for your >>>>>>>>>>>>>>>>>>>>>>>>> application above. >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> And then run csg_stat (or csg_boltzmann): >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/votca/votca/blob/master/csg-tutorials/propane/atomistic/run.sh#L22 >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> Christoph >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> There is >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> My aim is to generate the every bond length >>>>>>>>>>>>>>>>>>>>>>>>>> histogram >>>>>>>>>>>>>>>>>>>>>>>>>> Please provide me the suggestions. >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> Thanks & Regards >>>>>>>>>>>>>>>>>>>>>>>>>> Kankana Bhattacharjee >>>>>>>>>>>>>>>>>>>>>>>>>> Ph. D. Scholar >>>>>>>>>>>>>>>>>>>>>>>>>> Department of Chemistry >>>>>>>>>>>>>>>>>>>>>>>>>> Ashoka University >>>>>>>>>>>>>>>>>>>>>>>>>> Sonipat, Haryana >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> [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&;> >>>>>>>>>>>>>>>>>>>>>>>>>> 06/01/23, >>>>>>>>>>>>>>>>>>>>>>>>>> 04:51:51 PM >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, May 31, 2023 at 10:45 AM Christoph >>>>>>>>>>>>>>>>>>>>>>>>>> Junghans <[email protected]> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> On Tue, May 30, 2023 at 10:46 PM Kankana >>>>>>>>>>>>>>>>>>>>>>>>>>> Bhattacharjee <[email protected]> >>>>>>>>>>>>>>>>>>>>>>>>>>> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Ok sir. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> I have tried to perform boltzmann inversion >>>>>>>>>>>>>>>>>>>>>>>>>>>> after short (5 ps) atomistic MD run of propane. I >>>>>>>>>>>>>>>>>>>>>>>>>>>> am attaching the >>>>>>>>>>>>>>>>>>>>>>>>>>>> corresponding grompp.mdp file of the atomistic >>>>>>>>>>>>>>>>>>>>>>>>>>>> run, distributed bonded >>>>>>>>>>>>>>>>>>>>>>>>>>>> potential files, and boltzmann inverted bonded >>>>>>>>>>>>>>>>>>>>>>>>>>>> potential files. But, not >>>>>>>>>>>>>>>>>>>>>>>>>>>> understanding how these potential are helping in >>>>>>>>>>>>>>>>>>>>>>>>>>>> generating the itp file of >>>>>>>>>>>>>>>>>>>>>>>>>>>> CG propane. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> Well once you have the inverted potentials you >>>>>>>>>>>>>>>>>>>>>>>>>>> can use them in the CG run, *.pot is the VOTCA >>>>>>>>>>>>>>>>>>>>>>>>>>> format, which you have to >>>>>>>>>>>>>>>>>>>>>>>>>>> convert to xvg (see >>>>>>>>>>>>>>>>>>>>>>>>>>> https://www.votca.org/csg/preparing.html#exporting-the-table >>>>>>>>>>>>>>>>>>>>>>>>>>> ) >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> the table_a1 (a1 for Angle 1) and table_b1 (b1 >>>>>>>>>>>>>>>>>>>>>>>>>>> for Bond 1) in the propane tutorials were generated >>>>>>>>>>>>>>>>>>>>>>>>>>> this way: >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> https://github.com/votca/votca/tree/master/csg-tutorials/propane/ibi >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> And, the thing which I understood is that, >>>>>>>>>>>>>>>>>>>>>>>>>>>> boltzmann inversion is used for getting all atom >>>>>>>>>>>>>>>>>>>>>>>>>>>> inverted potential and >>>>>>>>>>>>>>>>>>>>>>>>>>>> force matching is used for getting non-bonded >>>>>>>>>>>>>>>>>>>>>>>>>>>> potentials. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> For you can use iterative boltzmann inversion >>>>>>>>>>>>>>>>>>>>>>>>>>> for the non-bonded interactions. >>>>>>>>>>>>>>>>>>>>>>>>>>> (Force-matching works for bonded interactions as >>>>>>>>>>>>>>>>>>>>>>>>>>> well, but VOTCA has implemented that) >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> CG propane itp (topol.top) file is available >>>>>>>>>>>>>>>>>>>>>>>>>>>> in ibi/imc methods part of votca. Can it be >>>>>>>>>>>>>>>>>>>>>>>>>>>> supplied in performing CG-MD >>>>>>>>>>>>>>>>>>>>>>>>>>>> simulation using GROMACS ? >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> If you run the propane tutorial after a couple >>>>>>>>>>>>>>>>>>>>>>>>>>> of steps you will have some tabulated potential >>>>>>>>>>>>>>>>>>>>>>>>>>> that you can use for 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&;> >>>>>>>>>>>>>>>>>>>>>>>>>>>> 05/31/23, >>>>>>>>>>>>>>>>>>>>>>>>>>>> 10:12:10 AM >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, May 31, 2023 at 10:10 AM Christoph >>>>>>>>>>>>>>>>>>>>>>>>>>>> Junghans <[email protected]> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Tue, May 30, 2023 at 10:33 PM Kankana >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Bhattacharjee < >>>>>>>>>>>>>>>>>>>>>>>>>>>>> [email protected]> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thank you sir. I would like to know, how can >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> one get gromacs compatible itp file for a Coarse >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> grained model using votca >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> It is all tabulated interaction, hence no itp >>>>>>>>>>>>>>>>>>>>>>>>>>>>> files. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> And the interactions are determined by IBI, >>>>>>>>>>>>>>>>>>>>>>>>>>>>> IMC or Force Matching, whatever you prefer. >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> 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&;> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 05/31/23, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 10:02:22 AM >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Wed, May 31, 2023 at 9:58 AM Christoph >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Junghans <[email protected]> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Sun, May 28, 2023 at 10:13 PM Kankana >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Bhattacharjee < >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> [email protected]> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Thanks a lot sir for your kind help. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I have gone through the topol.top file of >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> spce and propane model using ibi method. I >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> have doubts, how did you define >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the mass of the beads, charge, bond and angle >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> between beads in topol.top >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> file of the CG model ? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> For a center of mass mapping it is just the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> sum of the masses (and charges), but of course >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> you can do other mappings, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> too. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> In general making a coarse-grained model is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> more art than science. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 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&;> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 05/29/23, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 09:41:28 AM >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Fri, May 26, 2023 at 9:15 PM Christoph >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Junghans <[email protected]> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> On Thu, May 25, 2023 at 7:23 AM Kankana >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Bhattacharjee >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> <[email protected]> wrote: >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > Dear Sir, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > I am learning votca. Now, I have done >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> spce water model atomistic md run. In the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> spce/atomistic foolder, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> grompp.mdp contains integrator as "sd" . And, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> I used this settings for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> short MD run. Then, used csg_tool to compute >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> rdf of CG-CG beads and >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> compared with CG-CG with ibi. Then, I dint >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> understand the "Running ibi" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> part of the spce model. It has been asked to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> reduce the number of MD steps >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> in grompp.mdp and adjust the equilibration >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> time in the settings.xml file. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Exactly how to adjust this and why ? I have >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> skipped the "Running ibi" >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> option. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Well, the number of MD steps is in >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> grompp.mdp, while the equilibration >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> time is in settings.xml. Longer run will >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> give you smoother RDFs, and >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the system usually needs some time to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> equilibrate from the initial >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> condition, so you don't want to pick that >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> too short. In the tutorial >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> we ask folks to explore these options to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> get some feel for statistics. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > Second;y, I did force matching part >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> exactly. But, dint understand exactly what is >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> happening. Like, If I want to >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> generate gromacs compatible forcefield.itp >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> for a coarse grained model and >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> perform MD simulation using gromacs. THen, >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> how can I generate ttp file for >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> a molecule. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Force matching return a tabulated force >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> that can then be used to run >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> the coarse-grained simulation. Have a look >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> at the topol.top of the >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> spce/ibi example. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christoph >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > Thanks & Regards >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > Kankana Bhattacharjee >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > -- >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > 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/c6eaf8c8-1963-4772-9800-dc9d839dd0bbn%40googlegroups.com >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christoph Junghans >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Web: http://www.compphys.de >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 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/CAHG27e73xWx4bDHzx2AAxA%2B8OaQC%2B_6ru%2B7iACRsRWZrDJOoqQ%40mail.gmail.com >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christoph Junghans >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Web: http://www.compphys.de >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Christoph Junghans >>>>>>>>>>>>>>>>>>>>>>>>>>>>> Web: http://www.compphys.de >>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>>>>>>> Christoph Junghans >>>>>>>>>>>>>>>>>>>>>>>>>>> Web: http://www.compphys.de >>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>>>>>> Christoph Junghans >>>>>>>>>>>>>>>>>>>>>>>>> Web: http://www.compphys.de >>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>>> Christoph Junghans >>>>>>>>>>>>>>>>>>>>> Web: http://www.compphys.de >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>> [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, >>>>>>>>>>>>>>>>>>>>> 07:13:42 PM >>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>>>> Christoph Junghans >>>>>>>>>>>>>>>>>>>> Web: http://www.compphys.de >>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>> Christoph Junghans >>>>>>>>>>>>>>>>>> Web: http://www.compphys.de >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>> Christoph Junghans >>>>>>>>>>>>>>>>>> Web: http://www.compphys.de >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>>>> 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/CAHG27e4fdqGEwaOmCf%2BHbBk%2BQ%3DAyuJ35AGn011ji6CAjdYeAgg%40mail.gmail.com >>>>>>>>>>>>>>>>>> <https://groups.google.com/d/msgid/votca/CAHG27e4fdqGEwaOmCf%2BHbBk%2BQ%3DAyuJ35AGn011ji6CAjdYeAgg%40mail.gmail.com?utm_medium=email&utm_source=footer> >>>>>>>>>>>>>>>>>> . >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> -- >>>>>>>>>>>>>>>> Christoph Junghans >>>>>>>>>>>>>>>> Web: http://www.compphys.de >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>> -- >>>>>>>>>>>>>> Christoph Junghans >>>>>>>>>>>>>> Web: http://www.compphys.de >>>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> -- >>>>>>>>>>> Christoph Junghans >>>>>>>>>>> Web: http://www.compphys.de >>>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>>>>>>>> -- >>>>>>>>> Christoph Junghans >>>>>>>>> Web: http://www.compphys.de >>>>>>>>> >>>>>>>> >>>>> >>>>> -- >>>>> Christoph Junghans >>>>> Web: http://www.compphys.de >>>>> >>>> >>> >>> -- >>> Christoph Junghans >>> Web: http://www.compphys.de >>> >> > > -- > Christoph Junghans > Web: http://www.compphys.de > -- 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/CAMNJFV%3D0YH5UCfNA%2B7MP2Rtjv0TNMp%3D_3cB%2BAq5%3DUbjThKQrWA%40mail.gmail.com.
