2017-05-25 9:51 GMT-06:00 M. Chakraborty <[email protected]>: > Hello, > I am trying run a coarse-grained simulation of methanol. I am using a two > bead representation of methanol (A- CH3, B- OH). When I ran grompp I > encountered the following error: > > > Fatal error: > Group A referenced in the .mdp file was not found in the index file. > Group names must match either [moleculetype] names or custom index group > names, in which case you must supply an index file to the '-n' option > of grompp. > > I consulted the hexane and propane tutorials, and realized that I have to > provide an index file while running grompp. However, gmx make_ndx -f > conf_cg.gro g gives me an index.ndx file where indices of [A] and [B] are > not listed. I am wondering if I am missing a special directive during the > make_ndx command or do I actually have to add the two blocks of [A] and [B] > indices myself. I am adding my conf_cg.gro and cgtop.top file for > reference. Thanks. When running make_ndx, you need to make a group "A" and "B", e.g. using "a A*" and then "name 3 A" for the "A" group.
Christoph > > Regards, > M. Chakraborty > > -- > 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.
