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 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.
