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.
