2013/7/7 郭志成 <[email protected]>: > Dear Christoph, > > Thanks for your help. It is working now. There is another question about the > coarse-grained topology file as shown in methanol/ibi/topol.top and > propane/ibi/topol.top. I have been familiar with the atomistic topology. > Therefore, I want to know how to determine these parameters related to > coarse-grained beads (e.g. c6, c12, bonds and angles items).Whether the > specification of these parameters are arbitrary. No, it is not arbitrary, if you are using tables in gromacs the values c6 and c12 are the pre-factors for the table column 4/5 (c6) and 6/7 (c12). (also see gromacs manual section 4.2.13) In VOTCA we only use column 6 and 7 for IBI hence we set c12 to 1.0 (and c6 to 0, which not 100% necessary as column 4,5 are filled with zeros).
In some cases (e.g. spce/tf) it is useful to have c6 and c12 set to something non-trivial. Christoph > > > > Sincerely, > > Zhicheng > > > > 2013/7/8 Christoph Junghans <[email protected]> >> >> 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 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.
