[gmx-users] Strange results
Jordi Camps
jcamps at lsi.upc.edu
Thu Sep 8 15:52:18 CEST 2005
Hello,
I'm sure it is 3nm. Is the output of g_rms and is given in nm. The proteins
that I simulated are not dimers. The only have one chain. I can send you the
file that I used for the simulation, but is for 24 processors. So I will
generate a new one for only one processor.
Because of the file is large for a mail (1860005 bytes), I will put the file
on our web server. You can access the files requested at
http://mmb.pcb.ub.es/~jcamps/data.tar.gz
Inside the compressed file are two folders: GROMOS and OPLS, and in each one
are the .tpr file for one processor (generated with the same input than the
ones used in production for 24 processors), and 3 xvg files with the rms,
rgyr and potential energy for each forcefield.
>From the graphs you will see that the Gromos simulation rms stays at about
0.3-0.4 nm, but OPLS rms stabilizes quickly at about 4 nm.
Thank you for your help,
--
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. : 934 134 037
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 20:58
> Para: Discussion list for GROMACS users
> Asunto: RE: [gmx-users] Strange results
>
> 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.htm
> > > l
> > > >
> > > > _______________________________________________
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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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> --
> 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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