[gmx-users] Chloride parameters in ffgmx

[hugo verli]

Yes,

the geometry of chloroform moleculas is ok, as well as the box.

Hugo.

> > 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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MSc. Hugo Verli
Centro de Biotecnologia
Universidade Federal do Rio Grande do Sul