2013/7/4 郭志成 <[email protected]>: > And, how can I generate other intercations table.xvg for gromacs. I don't really understand your question!
For the interactions, which you iterate on an no initial guess is need, you just need the rdf. For all others (fixed) interaction, you will need a table. Manual describes this procedure for bonded interaction in some details, for non-bonded interactions use CG-CG.pot.new from $ csg_call --ia-name CG-CG --options settings.xml --ia-type non-bonded prepare_single ibi together with $ csg_call convert_potential gromacs CG-CG.pot.new table_CG_CG.xvg to convert CG-CG.pot.new to table_CG_CG.xvg. > > 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). >>> >>> 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. > 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.
