[gmx-users] crystals of KCl during simulation

[moura at ufscar.br]

Hi Rebeca,

I found out a few years ago that OPLS parameters for Na+ were inadequate
for my simulations on surfactants aggregation due to the formation of
stable (and unrealistic) ionic bridges. I got better  structures using
Aqvist's parameters (available in GROMACS), maybe you could try these
parameters for K+ as well.

please let me know if that works.

best regards,

André


>
> Yes, I use PME.
>
>> Date: Mon, 1 Jun 2009 19:34:27 +0200
>> From: spoel at xray.bmc.uu.se
>> To: gmx-users at gromacs.org
>> Subject: Re: [gmx-users] crystals of KCl during simulation
>>
>> Rebeca García Fandiño wrote:
>> > Thank you very much for your answer. I have read some recent
>> literature,
>> > and you are right, it is a problem about the parameters for ions in
>> Amber.
>> >
>> > I have found this paper:
>> > Parameters of Monovalent Ions in the Amber-99 Forcefield: Assesment of
>> > Inaccuracies and Proposed Improvements
>> > http://pubs.acs.org/doi/abs/10.1021/jp0765392
>> >
>> > There, they simulate nucleic acids using a combination of Amber and
>> > OPLS sigma and epsilon for the ions. I have tried that in the case of
>> my
>> > protein, just changing the ion sigma and epsilon in the topology by
>> > those corresponding to OPLS, but I still observe aggregation for the
>> ions.
>> >
>> > Would this combination of Amber and OPLS have any kind of potential
>> > problem during the simulation? Has anybody any idea to avoid this type
>> > of artefact?
>>
>> Just checking, do you use PME? (You should...)
>> >
>> > Thank you very much in advance,
>> >
>> > Rebeca.
>> >
>> > > To: gmx-users at gromacs.org
>> > > Subject: Re: [gmx-users] crystals of KCl during simulation
>> > > Date: Mon, 1 Jun 2009 14:34:55 +0200
>> > > From: baaden at smplinux.de
>> > >
>> > >
>> > > Hi,
>> > >
>> > > regafan at hotmail.com said:
>> > > >> [..] but after equilibration I have observed that KCl is
>> > aggregating, like
>> > > >> if it was making crystals. When I used NaCl instead KCl, this not
>> > > >> happened.
>> > >
>> > > >> Does anybody has any idea about the reason of the behaviour of
>> KCl in
>> > > >> the simulation?
>> > >
>> > > This even does happen with Amber :) So my guess is you correctly
>> > transferred
>> > > the parameters, but stumbled upon an artefact. If you check the
>> recent
>> > > literature you may notice that many publications with Amber using K+
>> > > only employ minimal (neutralising) salt conditions as a workaround.
>> At
>> > > least this is what we did recently [1].
>> > >
>> > > Marc Baaden
>> > >
>> > > [1] Interactions between neuronal fusion proteins explored by
>> molecular
>> > > dynamics, Biophys.J.94, 2008, 3436-3446.
>> > > http://dx.doi.org/10.1529/biophysj.107.123117
>> > >
>> > > --
>> > > Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris
>> > > mailto:baaden at smplinux.de - http://www.baaden.ibpc.fr
>> > > FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217
>> > >
>> > >
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>>
>> --
>> David.
>> ________________________________________________________________________
>> David van der Spoel, PhD, Professor of Biology
>> Dept. of Cell and Molecular Biology, Uppsala University.
>> Husargatan 3, Box 596, 75124 Uppsala, Sweden
>> phone: 46 18 471 4205 fax: 46 18 511 755
>> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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