[gmx-users] Charge groups in poly methyl methacrylic acid

Debadutta Prusty debaduttaprusty1.2015 at u.northwestern.edu
Wed Jun 6 05:01:46 CEST 2018

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 ?

Debadutta Prusty

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