Thanks again for your help. On Thursday, 25 May 2017 13:13:04 UTC-4, Christoph Junghans wrote: > > 2017-05-25 9:51 GMT-06:00 M. Chakraborty <[email protected] <javascript:>>: > > > 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] <javascript:>. > > To post to this group, send email to [email protected] > <javascript:>. > > 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 >
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