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

[David van der Spoel]

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.
http://www.icm.uu.se