2013/7/6 Zhicheng <[email protected]>: > Dear Christoph, > I apologize to you for my question. I have known how to get the tabulated > potential for bonded and non-bonded interactions.The table.xvg in > methanol/ibi you metioned is the file required by gromacs even if there are > no other interactions. My question is that how to generate this file. table.xvg isn't used anywhere, so you could use a file with zeros (like it is done in spce/ibi and the other examples), which I think is the safest. Where the table.xvg in methanol/ibi cames from, I don't remember, it seems to be simple BI potential.
> Whether is it similar to bonded or non-bonded interaction. Non-bonded tables have 7 columns while bonded tables have 3 columns. Bonded tables usually come from a Boltzmann inversion of the bonded distribution. > In addition, what > is the type of interaction represented by table.xvg because that the > interaction between the CG beads in methanol/ibi is given as > table_CG_CG.xvg. Like I said before table.xvg isn't used in this simulation, but gromacs uses it for the interaction of the "rest" energy group. Gromacs require table.xvg, even if the rest group is empty. In the case methanol/ibi the rest group is empty as the whole system belongs to the CG energy group (see index.ndx) and the CG-CG interaction is covered by a special interaction (grompp.mdp: energygrp_table = CG CG). table.xvg could be useful for a multi-component system, where only one interactions is iterated and all the others are covered normal LJ interactions. Christoph > > > > Sincerely, > Zhicheng > > 在 2013年7月6日星期六UTC+8上午12时01分18秒，Christoph Junghans写道： >> >> 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. > > -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. 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