[gmx-users] Re: gmx-users Digest, Vol 62, Issue 4

[Alan Chen]

Hi Rebeca:

If you wish to replicate the settings of 

http://pubs.acs.org/doi/abs/10.1021/jp0765392

(Aqvist's ions in AMBER) then you need the following LJ cross-types specified in your non-bonded forcefield or topology file, which were generated using geometric mixing rule instead of the (AMBER) additive mixing rule.

amber99_31     amber99_30  1  3.83554389e-01   7.56034201e-02 ;Na-Cl jorgensen CL
amber99_51     amber99_30  1  4.66877340e-01  2.60065255e-02 ;K-Cl jorgensen CL
amber99_53     amber99_30  1  5.44666722e-01  1.29237407e-02 ;Cs-Cl jorgensen CL
amber99_30     amber99_30  1  4.41724e-01     4.92833e-01  ;Cl-Cl (jorgensen)
amber99_31     amber99_31  1  3.33045e-01     1.1598e-02   ;Na-Na
amber99_51     amber99_51  1  4.93463e-01     1.37235e-02  ;K-K
amber99_53     amber99_53  1  6.716e-01       3.38904e-04  ;Cs-Cs

To clear up some possible confusion, it should be noted that recent OPLS forcefields include Aqvist's ions by default for use with simulations with TIP3P water, and the OPLS ion parameters others are referring to are officially considered obsolete. Jorgensen has also published ions for use with TIP4P using the Aqvist paradigm, although I do not have any experience using these parameters.

Hope it helps your aggregation problems!

Alan Chen


>   
>>  
>>  
>>  > Date: Mon, 1 Jun 2009 14:52:35 -0300
>>  > Subject: RE: [gmx-users] crystals of KCl during simulation
>>  > From: moura at ufscar.br
>>  > To: gmx-users at gromacs.org
>>  >
>>  > 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
>>  > >> > >
>
>