Dear Christoph, Thanks for your patient interpretation. I had a misunderstanding about initial guess of non-bonded tabulated potential and other interactions (table.xvg)
2013/7/5 Christoph Junghans <[email protected]> > 2013/7/4 郭志成 <[email protected]>: > > Hi Christoph, > > Thanks for your reply. Hmm, you're right that it is more quicker and > easier > > to run IBI using gromacs than espresso. As mentioned above, the initial > > tabulated potential for bonded interacation directly can be obtained > using > > csg_boltzmann tool, however, initial guess of tabulated potential for > > non-bonded interaction can not be generated by csg_boltzamnn tool. Thus, > I > > want to know how to get the initial non-bonded tabulated potential > > (csg-tutorial/methanol/ibi/table.xvg) through calculating rdf in VOTCA. > You don't need to provide an initial guess. VOTCA is doing that > automatically, you could do the same manually using: > $ csg_call --ia-name CG-CG --options settings.xml --ia-type non-bonded > prepare_single ibi > (change the "CG-CG" to name of your interaction) > This will generate a CG-CG.pot.new, which is the initial guess > calculated from the rdf. You could preprocess that file and give it to > Votca as initial guess (CG-CG.pot.in <http://cg-cg.pot.in/>). > > Please don't confuse table.xvg with an initial guess. The interaction > between the CG beads in methanol/ibi is given as table_CG_CG.xvg to > gromacs (see the xml settings file). table.xvg is used for all other > interactions, which are not covered by special tables (table_X_Y.xvg). > Even if there are no other interactions gromacs will need a table.xvg > file (this might has changed in gromacs 4.6). None of our tutorials > actually uses table.xvg, this is just a gromacs specialty. > > Christoph > > > > > Sincerely, > > Zhicheng > > 2013/7/3 Christoph Junghans <[email protected]> > >> > >> 2013/7/3 Zhicheng <[email protected]>: > >> > Hi Christoph, > >> > > >> > I retried the methanol/ibi_espresso tutorial and modified the bead > >> > interaction of lennard-jones (inter 0 0 lennard-jones 1.0 1.0 1.12246 > >> > 0.25 > >> > 0.0 ) to replace the tabulated potential (inter 0 0 tabulated > >> > "table_CG_CG.tab" ) in generate.tcl. However, I got the following > error > >> > message: > >> > > >> > > >> > property not found: table > >> Like I said before the scripts in generate_esp_from_gro are only to > >> generate espresso input data from gromacs input data. > >> (It basically generates conf.esp.gz from conf.gro) > >> If you have gromacs input data already just use gromacs to do IBI, it > >> is easier and quicker! > >> > >> > > >> > In my opinion, it means that the IBI procedure interfaced with > espresso > >> > only > >> > requires tabulated potential other than another type of interaction > >> > (such as > >> > lennard-jones). Thus, we have to specify the initial guess of > tabulated > >> > potential (table_CG_CG.tab). Is that right? > >> No, table_CG_CG.tab is generated from the initial rdf. > >> > >> To run IBI using Espresso just execute run.sh in methanol/ibi_espresso. > >> You might need to modify settings.xml if your Espresso binary is named > >> differently. > >> run.sh execute csg_inverse, which then calls Espresso. > >> > >> Remember to use the updated conf.esp.gz from: > >> > >> < > https://csg-tutorials.votca.googlecode.com/hg/methanol/ibi_espresso/conf.esp.gz > > > >> > >> Christoph > >> > > >> > Best Regards! > >> > > >> > Zhicheng > >> > 在 2013年6月28日星期五UTC+8下午10时49分24秒，Christoph Junghans写道： > >> >> > >> >> 2013/6/28 Zhicheng <[email protected]>: > >> >> > Dear all: > >> >> > > >> >> > The "hist" ("tab") command within csg_boltzmann tools to generate > the > >> >> > distribution function (tabulated potential), after post-processing, > >> >> > can > >> >> > be > >> >> > used to derive bonded interaction ( e.g *.dist.tgt table_a1.tab > >> >> > table_b1.tab > >> >> > in csg-tutorials/propane/ibi_espresso). However, the tabulated > >> >> > potential > >> >> > required by non-bonded interaction can't obtain using this method. > >> >> > Therefore, I want to know how to generate the tabulated potential > for > >> >> > non-bonded interaction ( such as table_CG_CG.tab in > >> >> > csg-tutorials/methanol/ibi_espresso/generate_esp_from_gro). I will > be > >> >> > appreciative if anyone can help me! > >> >> I think you mixing up two thing here. > >> >> > >> >> 1.) csg_inverse will generate table_CG_CG.tab during IBI procedure > >> >> for you, the initial potential is calculated out of the rdf > >> >> (rdf_methanol.xvg). So for IBI there is no initial table_CG_CG.tab > >> >> needed. > >> >> 2.) The files in generate_esp_from_gro are converts from gromacs > input > >> >> to espresso input (see generate.tcl). This was mainly done to allow > >> >> user to compare the behavior of different simulation back-ends > >> >> (espresso vs gromacs). In a real world study, there are very few > cases > >> >> where one would convert gromacs input files to espresso instead of > >> >> simply using gromacs directly. > >> >> > >> >> Christoph > >> >> > > >> >> > Best Regards! > >> >> > > >> >> > Zhicheng > >> >> > > >> >> > -- > >> >> > 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 post to this group, send email to [email protected]. > >> >> > Visit this group at http://groups.google.com/group/votca. > >> >> > For more options, visit https://groups.google.com/groups/opt_out. > >> >> > > >> >> > > >> >> > >> >> > >> >> > >> >> -- > >> >> Christoph Junghans > >> >> Web: http://www.compphys.de > >> > > >> > -- > >> > 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 post to this group, send email to [email protected]. > >> > Visit this group at http://groups.google.com/group/votca. > >> > For more options, visit https://groups.google.com/groups/opt_out. > >> > > >> > > >> > >> > >> > >> -- > >> Christoph Junghans > >> Web: http://www.compphys.de > >> > >> -- > >> 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/1ab9M7DmThk/unsubscribe. > >> To unsubscribe from this group and all its topics, send an email to > >> [email protected]. > >> > >> To post to this group, send email to [email protected]. > >> Visit this group at http://groups.google.com/group/votca. > >> For more options, visit https://groups.google.com/groups/opt_out. > >> > >> > > > > -- > > 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 post to this group, send email to [email protected]. > > Visit this group at http://groups.google.com/group/votca. > > For more options, visit https://groups.google.com/groups/opt_out. > > > > > > > > -- > Christoph Junghans > Web: http://www.compphys.de > > -- > 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/1ab9M7DmThk/unsubscribe. > To unsubscribe from this group and all its topics, send an email to > [email protected]. > To post to this group, send email to [email protected]. > Visit this group at http://groups.google.com/group/votca. > For more options, visit https://groups.google.com/groups/opt_out. > > > -- You received this message because you are subscribed to the Google Groups "votca" group. 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