And, how can I generate other intercations table.xvg for gromacs. Sincerely, Zhicheng
2013/7/5 郭志成 <[email protected]> > 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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