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 ? I want to know how to choose which method (ibi, imc) would be accurate to give accurate structural properties?
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 >> > -- 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/CAMNJFVmQZ9OnvbwWyAR%2Bms%3DB6kHcy7fy7KXuaV84J_5q3m27eg%40mail.gmail.com.
