[gmx-users] Strange results

[David]

On Wed, 2005-09-07 at 20:11 +0200, Jordi Camps wrote:
> 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.
Are you sure it is 3 nm? Isn't it a dimer dissociating?

> 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.
Otherwise if you have one example that unfolds relatively fast please
send me a (single processor) tpr file.


> 
> 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
> > > 
> > > _______________________________________________
> > > gmx-users mailing list
> > > gmx-users at gromacs.org
> > > http://www.gromacs.org/mailman/listinfo/gmx-users
> > > Please don't post (un)subscribe requests to the list. Use the www 
> > > interface or send it to gmx-users-request at gromacs.org.
> > --
> > 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
> > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > ++++++++++
> > 
> > _______________________________________________
> > gmx-users mailing list
> > gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please don't post (un)subscribe requests to the list. Use the 
> > www interface or send it to gmx-users-request at gromacs.org.
> > 
> 
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the 
> www interface or send it to gmx-users-request at gromacs.org.
-- 
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++