2015-10-19 13:58 GMT-06:00 Chang Woon Jang <[email protected]>: > Dear Votca users, > > I am trying to understand the statement of "VOTCA cannot make multiple > molecules into one". > > I have three type molecules in my system. Therefore, there is one topol.top > and three itp files in order to account for the topologies of my system. Let's me clarify, VOTCA can handle multiple molecules and molecule types, but it cannot map multiple molecules into a single one, like it is the case for MARTINI's water model, where four atomistic water molecules go into one. The restriction isn't technical, but more theoretical as it isn't always clear, which molecule to combine into one and what to do if there aren't enough molecules around.
> > If I would like to use csg_inverse, do I need to combine three itp files > into topol.top file? The only thing VOTCA reads is the binary topology file (topol.tpr) and it doesn't matter if it was generated from one or three itp files. > > Furthermore, I got an error message during the csg_inverse run. > > ERROR > critical: 'gmx grompp -n index.ndx -f grompp.mdp -p topol.top -o topol.tpr > -c conf.gro' failed This is an gromacs error, just have a look at the end of inverse.log to see by grompp is failing. You could also go into step_001 and run 'gmx grompp -n index.ndx -f grompp.mdp -p topol.top -o topol.tpr' It might be as simple as you have forgotten to add the itp files to the filelist in setting.xml. > > I have a setting.xml, topol.top, three itp files, table.xvg, table_a1.xvg, > table_b1.xvg, grompp.mdp, conf.gro, index.ndx files. I mainly referred to > Hexane ibi tutorial. > > My system was built for arbitrary engineering polymer system. I created > molecules and manually set topologies in oplsaa.ff. csg_map and > csg_boltzmann have worked fine so far. > > However, for ibi, specifically csg_inverse, it does not work. Would you give > any advise for me? > > -- > 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 http://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 http://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
