[gmx-users] LJ Switch function in the CVS VERSION3.3_beta_20050202

[David van der Spoel]

On Fri, 2005-09-09 at 14:35 +0800, Mu Yuguang (Dr) wrote:
> Dear David,
> In this 3.3 version, GB model is fully implemented ?

I don't think so...

> 
> Dr. Yuguang Mu
> Division of Structural and Computational Biology
> School of Biological Sciences
> Nanyang Technological University
> 60 Nanyang Drive 
> Singapore 637551
> Tel: 63162885
> Fax: 67913856
>  
> 
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org
> [mailto:gmx-users-bounces at gromacs.org] On Behalf Of David
> Sent: Friday, September 09, 2005 2:20 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] LJ Switch function in the CVS
> VERSION3.3_beta_20050202
> 
> On Thu, 2005-09-08 at 18:35 -0400, Xuhui Huang wrote:
> > Dear Gromacs users,
> >     We noticed that the LJ switch function in the CVS Version
> > 3.3_beta_20050202 gives the wrong energy. We tested this with the
> > water system in the tutor. With the LJ switch function, the CVS
> > version gives the LJ(SR) energy of  9.28495e+02 kJ/mol, however, the
> > Gromacs 3.1.4 gives the energy of 2.00385e+03 kJ/mol. With the LJ cut-
> > off, both version gives the energy about 2.0e+03 kJ/mol.
> >    Does anyone notice this problem before? 
> 
> Somehow I recall that the functional for for switch changed. Since it is
> useless anyway (except for maybe an Argon system), don't wast any time
> on it.
> >    
> >    The following is our parameters about the LJ switch part in
> > the .mdp part,
> >    
> >    ; Method for doing Van der Waals
> >    vdw-type                 = Switch ;Cut-off
> >    ; cut-off lengths       
> >    rvdw-switch              = 0.75
> >    rvdw                     = 0.85
> >     
> >  
> >  
> > Thanks
> > Xuhui
> > _______________________________________________
> > 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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++