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.
