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.
