Dear Christoph, Your valuable answers are really helpful to getting used to VOTCA and doing CG simulation. I will scrutinize gromacs topology file.
Thank you very much. Best regards, Changwoon Jang On Wed, May 4, 2016 at 2:58 PM, Christoph Junghans <[email protected]> wrote: > 2016-05-04 11:26 GMT-06:00 Chang Woon Jang <[email protected]>: > > Dear Christoph, > > > > Thank you very much. Therefore, if I use 3 different bond potentials, > I > > need to specify the tabulated potentials in topol.top file. > > > > ex., A-B (1-2) : table_b1.xvg, B-C (2-3) : table_b2.xvg, D-E (6-7) : > > table_b3.xvg > > > > [ bonds ] > > > > 1 2 8 1 1.0 > > 2 3 8 2 1.0 > > 6 7 8 3 1.0 > > > > > > fourth column in [ bonds ] section 1 2 3 is the information which > tabulated > > potential is used. > Yes, but remember the [bonds] section is on a per-molecule basis, i.e. > if you have two molecules (like you indicated above) you will need two > [bonds] sections one in each molecule topology section. > > > > > > > This question is more likely to Gromacs. > And yeah, this is more a question for the Gromacs users mailing list! > > > > > Thank you. > > > > Best regards, > > Changwoon Jang > > > > > > > > On Wed, May 4, 2016 at 1:04 PM, Christoph Junghans <[email protected]> > > wrote: > >> > >> 2016-05-04 8:07 GMT-06:00 Chang Woon Jang <[email protected]>: > >> > Dear Votca Users, > >> > > >> > I have very simple question. I have two molecules in a system. The > >> > first > >> > molecule consists of five beads (A-B-C-B-A) and three bead types, and > >> > the > >> > second molecule has three beads (D-E-D) and two bead types. Thus, I > have > >> > three bond and angle potentials, table_b1.xvg, table_b2.xvg, > >> > table_b3.xvg, > >> > table_a1.xvg, table_a2.xvg, and table_a3.xvg. > >> > > >> > table_b1.xvg : A-B > >> > table_b2.xvg : B-C > >> > table_b3.xvg : D-E > >> > table_a1.xvg : A-B-C > >> > table_a2.xvg : B-C-B > >> > table_a3.xvg : D-E-D > >> > > >> > > >> > I ran IBI to obtain non-bonded potentials. How do IBI calculation > figure > >> > out > >> > which tabulated potentials matching which bond and angle? Should the > >> > topology file configure the potentials? > >> In the gromacs' topol.top, each molecule has a bonds and angle block, > e.g. > >> [ bonds ] > >> 1 2 8 1 1.0 > >> 2 3 8 1 1.0 > >> > >> [ angles ] > >> 1 2 3 8 1 1.0 > >> > >> The "8" in column 3 (for bonds) and 4 (for angles) means use a > >> tabulated potential. The "1" in column 4 (and 5 for angles) is the > >> table number, i.e. the number in filename e.g. table_b1.xvg > >> > >> See Section 4.2.14 of the gromacs manual > >> (ftp://ftp.gromacs.org/pub/manual/manual-5.0.7.pdf) for details. > >> > >> 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. > > > > > > > > > > -- > > 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. 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