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 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.
