Hi everyone, I am new to gromacs and hence, this question might be naive. How does one go about assigning charge groups while creating new monomer topologies in .rtp files? What I gather from looking at similar posts is that the net charge of a charge group should be an integer (zero for a neutral group and positive/negative for charged groups). However, this rule does not seem to be that straight-forward in many cases. For a polymer PMAA ( https://en.wikipedia.org/wiki/Poly(methacrylic_acid)), the charged groups can be CO2H, CH3,CH2. According to opls fields, these groups have a net zero charge. However, the remaining carbon atom, which does not have a hydrogen, has a net charge of -0.02 if I use opls_139 (C in alkane). Is there a way around this problem ?
Thanks, Debadutta Prusty -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
