On Mon, Nov 14, 2022 at 5:20 AM Victor Nazarychev <[email protected]> wrote: > > Dear Christoph, > > I tried parameterising non-bonded interaction in composite systems with > stacks containing the polymer (C-type beads) and graphene-like molecules > (A-type beads). > > To understand in what range, I should conduct force calculations, first I > calculated the target distribution A-A, A-C, C-C, please see > fig.SYS_all_targets.jpg. > > From these distributions, I understand that I should calculate the forces in > the range from 0 to 4 ns. Then, using settting_fm2.xml I started a > force-matching procedure. However, for C-C interactions, I got infinity > > #### Force matching residual #### > Chi_2[(kJ/(mol*nm))^2] = -nan > ################################# > > This should be a number: -nan > This should be a number: -7.13506 > This should be a number: -6.01957 > > I changed the ranges in which I calculated the forces (from 0 to 2, 3 or 3.5 > nm). Nevertheless, for the C-C interactions, the number was NAN. > > Maybe I should change some parameters in the setting file? Or should I > increase the box size? I am not the force-matching expert, so I will have to think about this a bit more carefully, but I am assuming the error is an artifact from the fact that the system isn't uniform.
Christoph > > Best wishes, > > Victor > > <cg> > > <fmatch> > <!--Number of frames for block averaging --> > <frames_per_block>6</frames_per_block> > <!--Constrained least squares?--> > <constrainedLS>0</constrainedLS> > </fmatch> > > <non-bonded> > <name>C-C</name> > <type1>C</type1> > <type2>C</type2> > <fmatch> > <min>0.0</min> > <max>4.0</max> > <step>0.01</step> > <out_step>0.005</out_step> > <res_output_coeff>5</res_output_coeff> > </fmatch> > </non-bonded> > > <non-bonded> > <name>A-A</name> > <type1>A</type1> > <type2>A</type2> > <fmatch> > <min>0.0</min> > <max>4.0</max> > <step>0.01</step> > <out_step>0.005</out_step> > <res_output_coeff>5</res_output_coeff> > </fmatch> > </non-bonded> > > <non-bonded> > <name>A-C</name> > <type1>A</type1> > <type2>C</type2> > <fmatch> > <min>0.0</min> > <max>4.0</max> > <step>0.01</step> > <out_step>0.005</out_step> > <res_output_coeff>5</res_output_coeff> > </fmatch> > </non-bonded> > > > </cg> > > пятница, 11 ноября 2022 г. в 10:35:24 UTC+3, Victor Nazarychev: >> >> Dear Christoph, >> >> Thank you very much. >> >> чт, 10 нояб. 2022 г. в 19:30, Christoph Junghans <[email protected]>: >>> >>> On Thu, Nov 10, 2022 at 5:01 AM Victor Nazarychev <[email protected]> >>> wrote: >>> > >>> > Dear Cristoph, >>> > >>> > Thank you for your help. >>> > >>> > среда, 9 ноября 2022 г. в 22:52:45 UTC+3, Christoph Junghans: >>> >> >>> >> On Wed, Nov 9, 2022 at 11:48 AM Victor Nazarychev <[email protected]> >>> >> wrote: >>> >> > >>> >> > Dear Votca users, >>> >> > >>> >> > I try to parametrize the non-bonded intecations in CG model using the >>> >> > ibi procedure for graphene molecules. However, when I build >>> >> > nanocomposite comprises polymer and graphene flakes is atomostic >>> >> > simulation stacks are formed between the graphene flakes. In this >>> >> > case, the target pair distribution function between CG atoms in >>> >> > graphene falls to 1 only on the end of box. please see the attached >>> >> > file. >>> >> > >>> >> > If I undesrtand it is imposible to acurate calculate potential between >>> >> > the atoms in stacks using ibi procedure due to the fact the rdf does >>> >> > not fall to one. >>> >> There are re-weighting techniques for these kind of systems, e.g. see >>> >> https://doi.org/10.1063/1.4742067 >>> >> >>> > I have a couple of clarifying questions. I did not find re-weighting >>> > techniques in the VOTCA, as I understand this approach has not been >>> > implemented yet? >>> Correct and most likely it will never get added. You will have to >>> overwrite the RDF calculator script with something that works for your >>> special case. >>> >>> >> >>> >> > However, could I calculate in some case this like potential for CG >>> >> > model with help of the force-matching? >>> >> I think force-matching could work as well. >>> >> >>> > >>> > If I use bonded potentials calculated by the ibi procedure, will >>> > calculating only nonbonded potentials with the help of force-matching be >>> > correct for my model? Or should I parametrize bonded and non-bonded >>> > potential together by means of force-matching? >>> >>> That depends on the system, so I don't know. >>> We mixed IB/IBI with force-matching in this paper >>> http://dx.doi.org/10.1002/mats.201100011 and it worked, but that isn't >>> a guarantee it will work for your system. >>> IBI reproduces the effective PMF while FM reproduces the average >>> force, which is not always the same. >>> >> If I understand the procedure csg_fmatch is not paralleled and can be used >> in single processor mode only? >> >> >> Best regards. >> Victor >> >>> >>> Christoph >>> >>> > >>> > Best regards, >>> > Victor >>> > >>> >> >>> >> Christoph >>> >> > >>> >> > Best regards, >>> >> > Victor >>> >> > >>> >> > -- >>> >> > 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/965daf19-3386-4355-8547-e651605e49b8n%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/fc03698e-076d-4702-8a3a-3c956bc3e079n%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 a topic in the >>> Google Groups "votca" group. >>> To unsubscribe from this topic, visit >>> https://groups.google.com/d/topic/votca/N0ETXMTYpBw/unsubscribe. >>> To unsubscribe from this group and all its topics, send an email to >>> [email protected]. >>> To view this discussion on the web visit >>> https://groups.google.com/d/msgid/votca/CAHG27e6nbZXSt17gPHgsHnOe8ySouq-1OS2BB4CsgANGwYiBwA%40mail.gmail.com. > > -- > 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/d142f494-d0e7-4138-a6c6-faedfedcb961n%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/CAHG27e7wTsybKvRkWKSXsHZv%2BbhLyb8y6ShB%2BMVpwye1iByrdg%40mail.gmail.com.
