[gmx-users] Chloride parameters in ffgmx

[David van der Spoel]

On Mon, 2003-04-28 at 16:48, Anton Feenstra wrote:
> hugo verli wrote:
> > 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 |
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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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