[gmx-users] Strange results

[Jordi Camps]

Hello,

I simulates 25 proteins with the 2 forcefields (50 simulation total). 300K,
1 atm, shake on hydrogens, pressure and temperature coupling methods are
berendsen and I used PME. The proteins and waters has been previously
equilibrated.
Then I run the Gromos simulation and I see how (almost all) the proteins
move but retain its shape. But when I run the OPLS simulation I see how
after so little time (500ps-2ns) the protein starts to unfold.
Most of the RMS for Gromos are about 0.3nm, but for OPLS is common 3-4nm.
The energies remain stable.
Which kind of details do you like to know? I could give you some files, in
case you want to see it, but they are large.

Thank you very much for your attention.

--
Jordi Camps Puchades
Supercomputing research, support and development
  Instituto Nacional de Bioinformatica (www.inab.org)
  Nodo Computacional GNHC-2 UPC-CIRI (inb.lsi.upc.edu)
  Barcelona Supercomputing Center Node (www.bsc.es)
c/. Jordi Girona 29               
Edifici Nexus II, despatx 113     Tel.  : 934 034 037
E-08034 Barcelona                 Fax   : 934 017 014
Catalunya (Spain)                 e-mail: jcamps at lsi.upc.edu

Team info:
http://www.inab.org/~malaga/MOWServ/services/HELP/MarcoBajo/team.html
 

> -----Mensaje original-----
> De: gmx-users-bounces at gromacs.org 
> [mailto:gmx-users-bounces at gromacs.org] En nombre de David
> Enviado el: miércoles, 07 de septiembre de 2005 19:50
> Para: Discussion list for GROMACS users
> Asunto: Re: [gmx-users] Strange results
> 
> On Wed, 2005-09-07 at 19:34 +0200, Jordi Camps wrote:
> > Hello!
> > 
> > I've been running some simulations with two forcefields: Gromos 
> > (G43a1) and OPLS-aa. I ran a solvated protein (exactly the 
> same input 
> > except for the different hydrogens due to the unified 
> forcefield) with 
> > the two forcefields and the results are quite different.
> > I usually see that the Gromos simulation works fine, but 
> the ones done 
> > with OPLS unfolds and give high RMS. The .mdp parameter 
> file has been 
> > the same for the two inputs, so similar results are expected.
> > 
> > Do you know if this behaviour is normal? Is there some problem with 
> > the OPLS forcefield?
> 
> Differences are expected, but not so large. See e.g. Van der 
> Spoel & Lindahl, J. Phys. Chem. B. 117 pp. 11178-11187 (2003)
> 
> Please give more details.
> > 
> > Thank you for your attention,
> > 
> > --
> > Jordi Camps Puchades
> > Supercomputing research, support and development
> >   Instituto Nacional de Bioinformatica (www.inab.org)
> >   Nodo Computacional GNHC-2 UPC-CIRI (inb.lsi.upc.edu)
> >   Barcelona Supercomputing Center Node (www.bsc.es)
> > c/. Jordi Girona 29               
> > Edifici Nexus II, despatx 113     Tel.  : 934 034 037
> > E-08034 Barcelona                 Fax   : 934 017 014
> > Catalunya (Spain)                 e-mail: jcamps at lsi.upc.edu
> > 
> > Team info:
> > 
> http://www.inab.org/~malaga/MOWServ/services/HELP/MarcoBajo/team.html
> > 
> > _______________________________________________
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> --
> David.
> ______________________________________________________________
> __________
> 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://xray.bmc.uu.se/~spoel
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