David van der Spoel
spoel at xray.bmc.uu.se
Thu Sep 14 16:22:14 CEST 2006
Navratna Vajpai wrote:
> Sorry for not so explicitly explaining the things.. Here it goes
> I have a nona peptide and I ran a MD of 20ns using OPLS-AA force field.
> when I used the OPLS-AA the phi angles came out to be -ve for three of
> the amino acids. which is stericaly not allowed. But when I ran it using
> GROMOS I found all the phi-psi combinations with a negative phi value
> distribution. But now I am lost as you have said it works only for
> GROMOS like force field. Why?
problem in the anaysis program (assuming you used g_rama). please use
> and if that so I have got -ve phi distribution for the other phi-psi plots.
> My other question remained unanswered even now. Is there any way really
> to judge which force field is to be chosen for particular type of analysis?
> Best regards
what do you mean with -ve ?
force field can be evaluated in many ways.
Start by checking this paper and references in them:
Hydration thermodynamic properties of amino Acid analogues: a systematic
comparison of biomolecular force fields and water models.
* Hess B,
* van der Vegt NF.
J Phys Chem B Condens Matter Mater Surf Interfaces Biophys. 2006 Sep
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
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://folding.bmc.uu.se
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