[gmx-users] Chloride parameters in ffgmx

[David van der Spoel]

On Tue, 2003-04-29 at 13:25, hugo verli wrote:
> Hi, 
> 
> following Anton suggestion I changed my Ab-initio charges by the gromos charges:
> 
>           Gromos          Ab-initio
>      C :  0.261            -0.102 
>      Cl: -0.087             0.034
> Density:  5.51846e+02       5.96717e+02
> 
> There is not a change in the density profile. Is there anything else than I
> can do?
> 
is the geometry correct?


> About the David comments, I'm not using a explicit H, but following the united
> atom proceeding. I thought that it was obligatory when using Gromacs
> forcefield. Should I do something different? 
> 
> Thanks for the suggestions,
> 
> Hugo.
> 
> > > > Hi,
> > > > 
> > > [...]
> > > 
> > > > The charges were obtained from Ab-initio calculations and the topology
> for the
> > > > chloroform made in PRODRG site.
> > > > 
> > > > Any suggestion? Could this error be due to atomic charges or to van der
> Waals
> > > > parameters (form chloride ion and not for covalent bound chlorine)?
> > > [...]
> > > 
> > > There is already chloroform in the Gromos forcefield, isn't it also
> > > already in the Gromacs? If not, you could probably simply take the
> > > Gromos parameters, at least for a good start.
> > > 
> > > Ab-initio charges are usually (a lot) higher than those used in the
> > > Gromos/Gromacs forcefields, for example, from page IV-271 GromOS
> > > manual, Cl charges are -0.087, C is 0.179 and H is 0.08. You can
> > > compare these to the charges you found from Ab-initio.
> > 
> > another subtle detail is when you have an explicit H in the model and
> > you use constraints... You will find that your molecule only has five
> > degrees of freedom left (iso 6), so your temperature is not correct.
> > 
> > You may be simulating at an effective temperature of 20% more than what
> > you think (i.e. Ekin should be divided by 6*nmol iso 5*nmol).
> > 
> > > -- 
> > > Groetjes,
> > > 
> > > Anton
> > >   _____________ _______________________________________________________
> > > |             |                                                       |
> > > |  _   _  ___,| K. Anton Feenstra                                     |
> > > | / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
> > > |(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
> > > | \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
> > > |             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
> > > |             | "If You See Me Getting High, Knock Me Down"           |
> > > |             | (Red Hot Chili Peppers)                               |
> > > |_____________|_______________________________________________________|
> > > 
> > > _______________________________________________
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> > -- 
> > Groeten, David.
> > ________________________________________________________________________
> > Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
> > 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://xray.bmc.uu.se/~spoel
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
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> 
> 
> 
> MSc. Hugo Verli
> Centro de Biotecnologia
> Universidade Federal do Rio Grande do Sul
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-- 
Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
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://xray.bmc.uu.se/~spoel
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