[gmx-users] 3.3beta vs 3.2 dispersion correction term
spoel at xray.bmc.uu.se
Thu Jul 28 17:00:46 CEST 2005
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
I'm afraid that doesn't explain it however.
> 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:
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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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