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. This question is more likely to Gromacs. 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.
