[gmx-users] 3.3beta vs 3.2 dispersion correction term

[David]

On Thu, 2005-07-28 at 10:38 -0400, Sukit Leekumjorn wrote:
> Thank your for your reply, David
> 
> I downloaded the beta version on July 8 2005 from the CVS usage 
> website.  I noticed that the heading of the program is in VERSION 
> 3.3_beta_20050202. I am not certain if this is the latest version. If it 
> is not, can you please let me know the patches for the latest version.
> 
if you used CVS then you can get later patches by typing 
cvs update
I'm afraid that doesn't explain it however.

> Sukit
> 
> David wrote:
> 
> >On Wed, 2005-07-27 at 16:58 -0400, Sukit Leekumjorn wrote:
> >  
> >
> >>Thank you for your reply, David
> >>
> >>Sorry about not comparing things one at a time.  I took your suggestion 
> >>and tried comparing both cutoff (rvdw=1 and rcoulomb=1.8) and pme 
> >>(rvdw=0.9 and rcoulomb=0.9) for both versions without corrections; and 
> >>it turns out to be almost exactly the same. I then took an additional 
> >>step to compare the pme simulation including the correction factor for 
> >>both versions.  Listed below is the total energy caculated in step 0.  
> >>You mentioned that the corrction factor in 3.2.1 version is not correct 
> >>and it is fixed in the 3.3B version, I am not sure if this is normal for 
> >>the correction factor to be 2 orders of magnitude higher, which greatly 
> >>effects the total energy of the system.
> >>
> >>3.2.1 cutoff: -1.71612e+6
> >>3.2.1 pme without correction: -1.69195e+6
> >>3.2.1 pme with correction: -1.69664e+6 (Disp Corr = -4.69360e+3)
> >>
> >>3.3B cutoff: -1.71385e+6
> >>3.3B pme without correction: -1.69413e+6
> >>3.3B pme with correction: -1.96249e+6 (Disp Corr = -2.68357e+5)
> >>    
> >>
> >I get different numbers (step 0 only):
> >PME with correction Total energy -1.73585e+06  (Disp corr  -3.54849e+04)
> >
> >Are you sure you have the latest version? There have been changes in
> >this code in april, see:
> >http://www.gromacs.org/features/changes33.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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