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

David van der Spoel spoel at xray.bmc.uu.se
Wed Jun 6 08:11:37 CEST 2018

Den 2018-06-06 kl. 05:01, skrev Debadutta Prusty:
> 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
This is not important anymore as long as you use PME and the appropriate 
shifting function. But your system does need to be neutral overall.

David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.

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