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. 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.
conf_cg.gro
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cgtop.top
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