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.
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 <http://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 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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 > 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