Dear Christoph, I can't get the parameters by fitting related properties (thermodynamics, hydrodynamics) because there are no experimental and theoretical results about the coarse-grained beads. Thus, how can I obtain the bonded prameters in topology file (e.g. bonds and angles items in propane/ibi/topol.top) 在 2013年7月8日星期一UTC+8下午12时45分52秒，Christoph Junghans写道： > > 2013/7/7 郭志成 <[email protected] <javascript:>>: > > 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] <javascript:>> > >> > >> 2013/7/6 Zhicheng <[email protected] <javascript:>>: > >> > 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 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