[gmx-users] Fwd: H2SO4 (H2PO4-) force field
David van der Spoel
spoel at xray.bmc.uu.se
Wed Jun 6 12:24:59 CEST 2018
Den 2018-06-06 kl. 10:22, skrev Ondrej Kroutil:
> 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.
Remove the 1-4 interaction between H and the O, it is often too strong
(due to poor force fields).
> I'll be glad for every .itp file you can offer me.
> Thank a lot and have a nice day.
> Ondřej Kroutil
> 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
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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