2016-06-28 11:21 GMT-06:00 Chang Woon Jang <[email protected]>: > Dear Christoph, > > I got the exclusion list as follows. > > I have 600 beads in 200 molecules for the coarsegraining > > List of exclusions: > 1 3 2 > 2 3 > 4 6 5 > 5 6 > 7 9 8 > 8 9 > 10 12 11 > 11 12 > 13 15 14 > 14 15 > 16 18 17 > 17 18 > 19 21 20 > 20 21 > 22 24 23 > 23 24 > ... > > > > Does this mean that rdf calculations in my system only excluded these bonded > pairs of interactions? It looks like bead #1 is excluded with #2 and #3. And bead #2 with #3. So it seems 1-3 interaction are excluded when the atomistic case gets mapped.
Did you check the exclusion in the coarse-grained setup (for IBI) as well? E.g. $ csg_dump --top topol_cg.xml --excl > Also, I have to exclude 1-3 pairs of interactions in lammps simulation? The output of csg_dump will show you what VOTCA sees and hence how the rdf is calculated, so check that first. Christoph > > Thank you. > > Best regards, > Changwoon Jang > > On Tue, Jun 28, 2016 at 1:03 PM, Christoph Junghans <[email protected]> > wrote: >> >> 2016-06-28 10:21 GMT-06:00 Chang Woon Jang <[email protected]>: >> > Dear Christoph, >> > >> > I have tried, >> > >> > 1. csg_stat --cg DGA.xml --top topol.xml --excl >> > 2. csg_stat --cg DGA.xml --top topol.tpr --excl >> > 3. csg_stat --cg DGA.xml --top topol.top --excl >> Sorry, I meant >> $ csg_dump --cg DGA.xml --top topol.xml --excl >> >> Christoph >> >> > >> > but those gave errors >> > >> > an error occurred: >> > error parsing command line: unrecognised option '%canonical_option%' >> > >> > How can I fix this problem? >> > >> > Thank you. >> > >> > Best regards, >> > Changwoon Jang >> > >> > >> > On Tue, Jun 28, 2016 at 12:11 PM, Christoph Junghans >> > <[email protected]> >> > wrote: >> >> >> >> 2016-06-28 8:34 GMT-06:00 Chang Woon Jang <[email protected]>: >> >> > Dear Christoph, >> >> > >> >> > Thank you for your response. How do I define exclusion of angle >> >> > in >> >> > mapping file, xml? >> >> The <angle> block below will automatically generate exclusions. >> >> Check it with: >> >> $ csg_stat --cg DGA.xml --top topol.xml --excl >> >> >> >> Christoph >> >> > >> >> > "csg_stat" needs two types xml files, one for molecule (DGA.xml) and >> >> > one >> >> > for >> >> > fmatch.xml. >> >> > >> >> > Where do I define the exclusion of angle or bond during rdf >> >> > calculation? >> >> > >> >> > The following is a molecule xml mapping file. famtch.xml from >> >> > tutorials >> >> > has >> >> > no exclusion information. >> >> > >> >> > Thank you. >> >> > >> >> > Best regards, >> >> > Changwoon Jang >> >> > >> >> > <cg_molecule> >> >> > <name>Other_chain_A</name> >> >> > <ident>Other_chain_A</ident> >> >> > <topology> >> >> > <cg_beads> >> >> > <cg_bead> >> >> > <name>A1</name> >> >> > <type>A</type> >> >> > <mapping>A</mapping> >> >> > <beads>1:DGA:O 1:DGA:O1 1:DGA:C 1:DGA:C1 1:DGA:C2 1:DGA:C3 >> >> > 1:DGA:C4 >> >> > 1:DGA:C5 1:DGA:C6 1:DGA:C7 1:DGA:C8 1:DGA:H 1:DGA:H1 1:DGA:H2 >> >> > 1:DGA:H3 >> >> > 1:DGA:H4 1:DGA:H5 1:DGA:H6 1:DGA:H7 1:DGA:H8 1:DGA:H9 >> >> > 1:DGA:H10</beads> >> >> > </cg_bead> >> >> > <cg_bead> >> >> > <name>A2</name> >> >> > <type>A</type> >> >> > <mapping>A</mapping> >> >> > <beads>1:DGA:O2 1:DGA:O3 1:DGA:C12 1:DGA:C13 1:DGA:C14 >> >> > 1:DGA:C15 >> >> > 1:DGA:C16 1:DGA:C17 1:DGA:C18 1:DGA:C19 1:DGA:C20 1:DGA:H17 1:DGA:H18 >> >> > 1:DGA:H19 1:DGA:H20 1:DGA:H21 1:DGA:H22 1:DGA:H23 1:DGA:H24 1:DGA:H25 >> >> > 1:DGA:H26 1:DGA:H27</beads> >> >> > </cg_bead> >> >> > <cg_bead> >> >> > <name>B1</name> >> >> > <type>B</type> >> >> > <mapping>B</mapping> >> >> > <beads>1:DGA:C9 1:DGA:C10 1:DGA:C11 1:DGA:H11 1:DGA:H12 >> >> > 1:DGA:H13 >> >> > 1:DGA:H14 1:DGA:H15 1:DGA:H16</beads> >> >> > </cg_bead> >> >> > </cg_beads> >> >> > <cg_bonded> >> >> > <bond> >> >> > <name>bond</name> >> >> > <beads> >> >> > A1 B1 >> >> > A2 B1 >> >> > </beads> >> >> > </bond> >> >> > <angle> >> >> > <name>angle</name> >> >> > <beads> >> >> > A1 B1 A2 >> >> > </beads> >> >> > </angle> >> >> > </cg_bonded> >> >> > </topology> >> >> > <maps> >> >> > <map> >> >> > <name>A</name> >> >> > <weights>16 16 12 12 12 12 12 12 12 12 12 1 1 1 1 1 1 1 1 1 1 >> >> > 1</weights> >> >> > </map> >> >> > <map> >> >> > <name>B</name> >> >> > <weights>12 12 12 1 1 1 1 1 1</weights> >> >> > </map> >> >> > </maps> >> >> > </cg_molecule> >> >> > >> >> > On Tue, Jun 28, 2016 at 10:00 AM, Christoph Junghans >> >> > <[email protected]> >> >> > wrote: >> >> >> >> >> >> 2016-06-27 15:33 GMT-06:00 Chang Woon Jang >> >> >> <[email protected]>: >> >> >> > Dear Christoph, >> >> >> > >> >> >> > >> >> >> > I am correcting the previous question. >> >> >> > >> >> >> > >> >> >> > Thank you for the clarification of the list. I have another >> >> >> > question. >> >> >> > A >> >> >> > molecule is bonded with A-B-C beads. The first bead (A) is mapped >> >> >> > with >> >> >> > atoms >> >> >> > from 1 to 22 and the second bead (B) is mapped with atoms from 23 >> >> >> > to >> >> >> > 31, >> >> >> > and >> >> >> > the third bead (C) is mapped with 32 to 53. In this exclusion >> >> >> > lists, >> >> >> > the >> >> >> > first bead (A) and third bead (C) seem to interact each other. It >> >> >> > look >> >> >> > like >> >> >> > that the atoms in A bead are fairly (not fully) interacted with >> >> >> > the >> >> >> > atoms in >> >> >> > C bead. Therefore, A-C radial distribution function seems to >> >> >> > include >> >> >> > 1-3 >> >> >> > (A-C) interactions somewhat. Is this correct? >> >> >> If the exclusion list says they are not excluded, so be it. You can >> >> >> add an angle between A-B-C (or a bond between A-C) in the mapping >> >> >> file >> >> >> to exclude them in rdf calculation. >> >> >> >> >> >> Christoph >> >> >> >> >> >> > >> >> >> > Thank you. >> >> >> > >> >> >> > Best regards, >> >> >> > Changwoon Jang >> >> >> > >> >> >> > On Mon, Jun 27, 2016 at 5:24 PM, Chang Woon Jang >> >> >> > <[email protected]> >> >> >> > wrote: >> >> >> >> >> >> >> >> Dear Christoph, >> >> >> >> >> >> >> >> Thank you for the clarification of the list. I have another >> >> >> >> question. A >> >> >> >> molecule is bonded with A-B-C beads. The first bead (A) is mapped >> >> >> >> with >> >> >> >> atoms >> >> >> >> from 1 to 22 and the second bead (B) is mapped with atoms from 23 >> >> >> >> to >> >> >> >> 31, and >> >> >> >> the third bead (C) is mapped with 32 to 53. In this exclusion >> >> >> >> lists, >> >> >> >> the >> >> >> >> first bead (A) and third bead (C) seem to interact each other. It >> >> >> >> look >> >> >> >> like >> >> >> >> that the atoms in A bead are fully interacted with the atoms in C >> >> >> >> bead. >> >> >> >> Therefore, A-C radial distribution function seems to include 1-3 >> >> >> >> (A-C) >> >> >> >> interactions. Is this correct? >> >> >> >> >> >> >> >> Thank you. >> >> >> >> >> >> >> >> Best regards, >> >> >> >> Changwoon Jang >> >> >> >> >> >> >> >> On Mon, Jun 27, 2016 at 5:03 PM, Christoph Junghans >> >> >> >> <[email protected]> >> >> >> >> wrote: >> >> >> >>> >> >> >> >>> 2016-06-27 13:37 GMT-06:00 Chang Woon Jang >> >> >> >>> <[email protected]>: >> >> >> >>> > Dear Christoph, >> >> >> >>> > >> >> >> >>> > >> >> >> >>> > I tested the following command. >> >> >> >>> > >> >> >> >>> > csg_dump --top topol.tpr --excl > exclusion_list >> >> >> >>> > >> >> >> >>> > In the exclusion_list file, the number are listed like >> >> >> >>> > >> >> >> >>> > I have 15000 beads in 300 molecules >> >> >> >>> > >> >> >> >>> > List of exclusions: >> >> >> >>> > 1 2 3 4 5 6 7 8 9 10 11 12 >> >> >> >>> > 2 3 4 5 6 7 9 >> >> >> >>> > 3 4 5 6 7 9 >> >> >> >>> > 4 5 6 7 9 >> >> >> >>> > 5 6 7 8 9 10 11 12 13 >> >> >> >>> > 6 7 8 9 10 11 12 >> >> >> >>> > 7 8 9 10 11 12 >> >> >> >>> > 8 9 >> >> >> >>> > 9 10 11 12 13 14 21 >> >> >> >>> > 10 11 12 13 >> >> >> >>> > 11 12 13 >> >> >> >>> > 12 13 14 15 16 19 21 22 >> >> >> >>> > 13 14 15 16 17 19 20 21 22 >> >> >> >>> > 18 13 14 15 16 17 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 >> >> >> >>> > 40 >> >> >> >>> > ... >> >> >> >>> > >> >> >> >>> > >> >> >> >>> > What do these numbers mean? The first line has 1 2 3 4 5 6 7 8 >> >> >> >>> > 9 >> >> >> >>> > 10 >> >> >> >>> > 11 >> >> >> >>> > 12. I >> >> >> >>> > do not know what this series of numbers. >> >> >> >>> It means, atom #1 is exclude with 2, 3, 4, ... >> >> >> >>> >> >> >> >>> > >> >> >> >>> > However, it seems that csg_stat excluded the pairs of beads >> >> >> >>> > directly >> >> >> >>> > bonded. >> >> >> >>> > Therefore, I do not need consider the 1-3 interactions in CG >> >> >> >>> > system >> >> >> >>> > in >> >> >> >>> > lammps. >> >> >> >>> > >> >> >> >>> > >> >> >> >>> > I am not sure why the density is higher than atomistic >> >> >> >>> > reference >> >> >> >>> > density >> >> >> >>> > when I do not apply 1-3 interactions. I have driven tabulated >> >> >> >>> > potential >> >> >> >>> > using ibi pressure correction method. Are there any >> >> >> >>> > suggestions >> >> >> >>> > for >> >> >> >>> > better >> >> >> >>> > CG simulation to fix the density? >> >> >> >>> > >> >> >> >>> > Thank you. >> >> >> >>> > >> >> >> >>> > Best regards, >> >> >> >>> > Changwoon Jang >> >> >> >>> > >> >> >> >>> > >> >> >> >>> > >> >> >> >>> > On Mon, Jun 27, 2016 at 3:15 PM, Christoph Junghans >> >> >> >>> > <[email protected]> >> >> >> >>> > wrote: >> >> >> >>> >> >> >> >> >>> >> 2016-06-27 12:58 GMT-06:00 Chang Woon Jang >> >> >> >>> >> <[email protected]>: >> >> >> >>> >> > Dear VOTCA users, >> >> >> >>> >> > >> >> >> >>> >> > I have a question about radial distribution functions >> >> >> >>> >> > from >> >> >> >>> >> > csg_stat. >> >> >> >>> >> > >> >> >> >>> >> > I have obtained radial distribution functions and used them >> >> >> >>> >> > for >> >> >> >>> >> > iterative >> >> >> >>> >> > boltzmann inversion to derive non-bonded tabulated >> >> >> >>> >> > potentials. >> >> >> >>> >> > After >> >> >> >>> >> > some >> >> >> >>> >> > iterations, the calculated radial distribution functions >> >> >> >>> >> > were >> >> >> >>> >> > well >> >> >> >>> >> > matched >> >> >> >>> >> > with reference RDF from csg_stat. Then, I used the obtained >> >> >> >>> >> > tabulated >> >> >> >>> >> > potentials for lammps simulations. >> >> >> >>> >> > >> >> >> >>> >> > From the lammps simulation with tabulated potentials, >> >> >> >>> >> > the >> >> >> >>> >> > liquid >> >> >> >>> >> > polymer >> >> >> >>> >> > system has higher density (1.3 g/cc) than the experimental >> >> >> >>> >> > density >> >> >> >>> >> > (1.07 >> >> >> >>> >> > g/cc) when I do not consider 1-3 bead pairs which are those >> >> >> >>> >> > separated by >> >> >> >>> >> > 3 >> >> >> >>> >> > bonds. However, when I applied 1-3 interactions, the >> >> >> >>> >> > simulational >> >> >> >>> >> > density is >> >> >> >>> >> > in good agreement with experimental density. >> >> >> >>> >> > >> >> >> >>> >> > I think that the reference radial distribution >> >> >> >>> >> > functions >> >> >> >>> >> > from >> >> >> >>> >> > csg_stat >> >> >> >>> >> > are calculated with pairs of beads directly bonded to each >> >> >> >>> >> > other >> >> >> >>> >> > as >> >> >> >>> >> > well >> >> >> >>> >> > as >> >> >> >>> >> > non-bonded pairs. >> >> >> >>> >> > >> >> >> >>> >> > Is this correct? >> >> >> >>> >> This depends on your topology file. csg_stat excludes bonds >> >> >> >>> >> and >> >> >> >>> >> angles >> >> >> >>> >> automatically. >> >> >> >>> >> However, if you have a topology file without bonds and >> >> >> >>> >> angles, >> >> >> >>> >> they >> >> >> >>> >> wont' be excluded. >> >> >> >>> >> To check use: >> >> >> >>> >> $ csg_dump --top topol.xml --excl >> >> >> >>> >> >> >> >> >>> >> Christoph >> >> >> >>> >> > >> >> >> >>> >> > Thank you. >> >> >> >>> >> > >> >> >> >>> >> > Best regards, >> >> >> >>> >> > Changwoon Jang >> >> >> >>> >> > >> >> >> >>> >> > >> >> >> >>> >> > -- >> >> >> >>> >> > 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 https://groups.google.com/group/votca. >> >> >> >>> >> > For more options, visit https://groups.google.com/d/optout. >> >> >> >>> >> >> >> >> >>> >> >> >> >> >>> >> >> >> >> >>> >> -- >> >> >> >>> >> 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 https://groups.google.com/group/votca. >> >> >> >>> >> For more options, visit https://groups.google.com/d/optout. >> >> >> >>> > >> >> >> >>> > -- >> >> >> >>> > 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 https://groups.google.com/group/votca. >> >> >> >>> > For more options, visit https://groups.google.com/d/optout. >> >> >> >>> >> >> >> >>> >> >> >> >>> >> >> >> >>> -- >> >> >> >>> 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 https://groups.google.com/group/votca. >> >> >> >>> For more options, visit https://groups.google.com/d/optout. >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> -- >> >> >> >> Best regards, >> >> >> >> Changwoon Jang, >> >> >> >> >> >> >> >> Postdoctoral Research Fellow >> >> >> >> Department of Chemical & Biological Engineering, Drexel >> >> >> >> University >> >> >> >> 3141 Chestnut Street, Philadelphia, PA 19104 >> >> >> >> >> >> >> >> Voice: (662) 617-2267 >> >> >> >> E-mail: [email protected] >> >> >> > >> >> >> > >> >> >> > -- >> >> >> > 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 https://groups.google.com/group/votca. >> >> >> > For more options, visit https://groups.google.com/d/optout. >> >> >> >> >> >> >> >> >> >> >> >> -- >> >> >> 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 https://groups.google.com/group/votca. >> >> >> For more options, visit https://groups.google.com/d/optout. >> >> > >> >> > >> >> > -- >> >> > 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 https://groups.google.com/group/votca. >> >> > For more options, visit https://groups.google.com/d/optout. >> >> >> >> >> >> >> >> -- >> >> 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 https://groups.google.com/group/votca. >> >> For more options, visit https://groups.google.com/d/optout. >> > >> > >> > >> > >> > -- >> > Best regards, >> > Changwoon Jang, >> > >> > Postdoctoral Research Fellow >> > Department of Chemical & Biological Engineering, Drexel University >> > 3141 Chestnut Street, Philadelphia, PA 19104 >> > >> > Voice: (662) 617-2267 >> > E-mail: [email protected] >> > >> > -- >> > 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 https://groups.google.com/group/votca. >> > For more options, visit https://groups.google.com/d/optout. >> >> >> >> -- >> 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 https://groups.google.com/group/votca. >> For more options, visit https://groups.google.com/d/optout. > > > > > -- > Best regards, > Changwoon Jang, > > Postdoctoral Research Fellow > Department of Chemical & Biological Engineering, Drexel University > 3141 Chestnut Street, Philadelphia, PA 19104 > > Voice: (662) 617-2267 > E-mail: [email protected] > > -- > 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 https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- 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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