Dear Christoph Thanks fou your suggestion. It is working now. Best Regards! Zhicheng Guo
2013/9/21 <[email protected]> > Today's Topic Summary > > Group: http://groups.google.com/group/votca/topics > > - Creating new lammps > tutorial<https://mail.google.com/mail/html/compose/static_files/blank_quirks.html#1413c2a0888e7ce7_group_thread_0>[7 > Updates] > - coarse-grained bead is bigger than half the > box<https://mail.google.com/mail/html/compose/static_files/blank_quirks.html#1413c2a0888e7ce7_group_thread_1>[1 > Update] > > Creating new lammps > tutorial<http://groups.google.com/group/votca/t/15e170f7162053a9> > > Scott Sides <[email protected]> Sep 18 01:46PM -0700 > > Christoph, > > I'd like to run the propane example with lammps (I've managed to get > the > spce example running and its very informative). > I've looked at the lammpsreader.cc page you've listed in > ...more<http://groups.google.com/group/votca/msg/e629f90aa9e788df> > > Back to > top.<https://mail.google.com/mail/html/compose/static_files/blank_quirks.html#1413c2a0888e7ce7_digest_top> > > > Christoph Junghans <[email protected]> Sep 18 03:20PM -0600 > > > I've looked at the lammpsreader.cc page you've listed in other > posts. I was > > wondering if you could give a quick outline of steps > > needed to bring the propane example up to speed with lammps. > ...more<http://groups.google.com/group/votca/msg/cf1a184fa2b3679d> > > Back to > top.<https://mail.google.com/mail/html/compose/static_files/blank_quirks.html#1413c2a0888e7ce7_digest_top> > > > Scott Sides <[email protected]> Sep 18 04:43PM -0700 > > Ok, I'll get on that. Couple of questions first > > I'm working from the manual for votca 1.2.3 and some of the commands > arent > working for the propane > tutorial. For example > > csg_gmxtopol --top > ...more<http://groups.google.com/group/votca/msg/c2d0a0a7f8ca488b> > > Back to > top.<https://mail.google.com/mail/html/compose/static_files/blank_quirks.html#1413c2a0888e7ce7_digest_top> > > > Chandan Choudhury <[email protected]> Sep 19 10:04AM +0530 > > Hi Scott, > > The --top flag takes tpr file as an input. > > Chandan > > > -- > Chandan kumar Choudhury > NCL, Pune > INDIA > > > ...more <http://groups.google.com/group/votca/msg/f72a6f26e54cc50a> > > Back to > top.<https://mail.google.com/mail/html/compose/static_files/blank_quirks.html#1413c2a0888e7ce7_digest_top> > > > Scott W Sides <[email protected]> Sep 18 10:37PM -0600 > > Indeed it does. However there is no such file in the tutorial. > > Sent from my iPhone so likely very brief > > ...more <http://groups.google.com/group/votca/msg/17cfd49e268f509d> > > Back to > top.<https://mail.google.com/mail/html/compose/static_files/blank_quirks.html#1413c2a0888e7ce7_digest_top> > > > Chandan Choudhury <[email protected]> Sep 19 11:04AM +0530 > > > > Indeed it does. However there is no such file in the tutorial. > > Dear Scott, > > The tpr file can be generated using the grompp executable of gromacs. > It > takes the input as structure (pdb/gro) > ...more<http://groups.google.com/group/votca/msg/d519b58bb8ecc39c> > > Back to > top.<https://mail.google.com/mail/html/compose/static_files/blank_quirks.html#1413c2a0888e7ce7_digest_top> > > > Christoph Junghans <[email protected]> Sep 19 02:58PM -0600 > > > > input format not supported: topol.top > > > is the result. The topol.top file is the cloest thing to a topology > file > > that the manual refers to. > Sorry, I wasn't really clear yesterday about how > ...more<http://groups.google.com/group/votca/msg/2eb81bd053f5cb27> > > Back to > top.<https://mail.google.com/mail/html/compose/static_files/blank_quirks.html#1413c2a0888e7ce7_digest_top> > > coarse-grained bead is bigger than half the > box<http://groups.google.com/group/votca/t/f7580c220d31396d> > > Christoph Junghans <[email protected]> Sep 18 02:58PM -0600 > > > means that there are 56 type A beads(A1,A2,……A56), 56 type B > > beads(B57,B58,……B112) and 2 type C beads(C1,C2) in coarse-grained > model of > > polymer. > There is an mistake in your mapping > ...more<http://groups.google.com/group/votca/msg/83bc7b793872c052> > > Back to > top.<https://mail.google.com/mail/html/compose/static_files/blank_quirks.html#1413c2a0888e7ce7_digest_top> > > -- > 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 http://groups.google.com/group/votca. > For more options, visit https://groups.google.com/groups/opt_out. > -- 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 http://groups.google.com/group/votca. For more options, visit https://groups.google.com/groups/opt_out.
