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

David spoel at xray.bmc.uu.se
Thu Jul 28 09:35:59 CEST 2005

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:
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

More information about the gromacs.org_gmx-users mailing list