[gmx-users] Chloride parameters in ffgmx
hugo at acd.ufrj.br
Tue Apr 29 13:24:01 CEST 2003
following Anton suggestion I changed my Ab-initio charges by the gromos charges:
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
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,
> > > Hi,
> > >
> > [...]
> > > The charges were obtained from Ab-initio calculations and the topology
> > > chloroform made in PRODRG site.
> > >
> > > Any suggestion? Could this error be due to atomic charges or to van der
> > > 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/ |
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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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