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

[Mu Yuguang (Dr)]

Dear David,
In this 3.3 version, GB model is fully implemented ?

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
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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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