[gmx-users] Fwd: H2SO4 (H2PO4-) force field

[Felipe Merino]

I've tried to generate parameters for H2PO4 for Charmm in 
https://cgenff.paramchem.org/ and the results were pretty OK (at least 
in terms of penalties).

Best

Felipe


On 06/06/18 10:22, Ondrej Kroutil wrote:
> Hi gromacs user,
> I have a favour to ask you.
> Does anybody have working model of sulfuric acid and/or H2PO4- (exactly
> these species with two OH groups)? I have tried to prepared one according
> to various articles:
>
> loukonen2010 - Enhancing effect of dimethylamine in sulfuric acid
> nucleation in the presence of water – a computational study
> canales2016 - A comparative molecular dynamics study of sulfuric and
> methanesulfonic acids
> ding2003 - Reliable potential for small sulfuric acid–water clusters
> margreitter2017 - Update on phosphate and charged post‐translationally
> modified amino acid parameters in the GROMOS force field -- dihedrals from
> this study were used with Loukonen params.
>
> but very often these models were unstable (or I should say my
> implementations of these models were unstable) and after several
> nanoseconds I got LINCS warning followed by a collapse of the oxoacid
> structure and forced end of the simulation. I attach my implementation of
> mentioned models and mdp file I use to run this simulations.
>
> I bet the problem is connected to dihedrals O-P(S)-O-H but I'm not hundred
> percent sure.
>
> I'll be glad for every .itp file you can offer me.
>
> Thank a lot and have a nice day.
>
>      Ondřej Kroutil
>
> https://scholar.google.cz/citations?user=vFX-JpoAAAAJ&hl=cs
>
> --
> Ondřej Kroutil
>          ,,              Faculty of Science
>     ----"))'             University of South Bohemia
>       OOO           Branisovska 1760, Ceske Budejovice, 370 05
>        OOO          The Czech Republic
>          | OO         E-mail:  okroutil at gmail.com
>> ------    O         Mobile:  +420 736 537 190

-- 
Felipe Merino,
Max Planck Institute for Molecular Physiology
Department of Structural Biochemistry
Otto-Hahn-Str. 11
44227 Dortmund
Phone: +49 231 133 2307

ORCID:  https://orcid.org/0000-0003-4166-8747
Publons: https://publons.com/a/1305699/
Researchgate: https://www.researchgate.net/profile/Felipe_Merino