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

[David]

On Wed, 2005-07-27 at 14:07 -0400, Sukit Leekumjorn wrote:
> Dear Gmx Users
> 
> I have used the dppc system (121,856 atoms) listed in the benchmark 
> section on the Gromacs website to test pme run for version 3.2 and 
> 3.3beta.. Based on a short simulation run of 5ps from one node, DispCorr 
> term seem to be a lot different than older version (see below).  I used 
> the same .mdp, .top and .gro given in the website.  Based on these two 
> runs, the area per headgroup from 3.2 version is about 0.63 nm2 (as 
> reported in many literatures) however the 3.3beta drop down to 0.57nm2. 
>  From the Feature/change section in the Gromacs website, I notice the 
> changes in dispersion correction for a large system. I was wandering if 
> the size of the system effect pme calculation in beta version, maybe 
> incorrect DispCorr term which effect the pressure of the system and then 
> the average area per headgroup of lipid?

First you need to be a bit more systematic and change one thing at a
time. The dispersion correction was wrong in 3.2. Therefore you'll have
to turn it off to compare codes. Make a tpr in 3.2.1 and use the same
tpr in 3.3

Second if you want to compare area per headgroup you'll have to check
many params such as pressure coupling and also have to simulate longer

Third you say you use PME, however you don't say which cut-offs you use
for Coulomb and VDW. Better to try without PME first.

> 
> Sukit Leekumjorn
> 
> 3.2 version
> 
>            Step           Time         Lambda
>               0        0.00000        0.00000
> 
> Grid: 39 x 40 x 13 cells
> 
> Testing x86 processor CPUID...
> CPU manufactured by Intel.
> 
> Testing x86 SSE capabilities...
> CPU and OS support SSE.
> Using Gromacs SSE single precision assembly innerloops.
> 
>    Rel. Constraint Deviation:  Max    between atoms     RMS
>        Before LINCS         0.012457   2313   2332   0.001510
>         After LINCS         0.000049    734    735   0.000006
> 
> Long Range LJ corr. to Epot:    -4693.6, Pres:   -78.1849, Vir:    28161.6
>    Energies (kJ/mol)
>           Angle    Proper Dih. Ryckaert-Bell.  Improper Dih.          LJ-14
>     8.73166e+04    2.91992e+04    5.71785e+04    4.00762e+03    2.09315e+05
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coulomb (LR)
>     1.88239e+05   -4.91021e+04   -4.69360e+03   -1.28225e+06   -1.26585e+06
>       Potential    Kinetic En.   Total Energy    Temperature Pressure (bar)
>    -2.02664e+06    3.30030e+05   -1.69661e+06    3.24380e+02    5.36413e+03
> 
> 3.3 beta version
> 
>            Step           Time         Lambda
>               0        0.00000        0.00000
> 
> Grid: 39 x 40 x 13 cells
> Configuring nonbonded kernels...
> Testing AMD 3DNow support... not present.
> Testing ia32 SSE support... present.
> 
> 
>    Rel. Constraint Deviation:  Max    between atoms     RMS
>        Before LINCS         0.012457   2313   2332   0.001510
>         After LINCS         0.000050    734    735   0.000006
> 
> Long Range LJ corr. to Epot:    -268357, Pres:   -4470.22, Vir:     268357
>    Energies (kJ/mol)
>           Angle    Proper Dih. Ryckaert-Bell.  Improper Dih.          LJ-14
>     8.73166e+04    2.91992e+04    5.71785e+04    4.00762e+03    2.09447e+05
>      Coulomb-14        LJ (SR)  Disper. corr.   Coulomb (SR)   Coul. recip.
>     1.88330e+05   -4.91021e+04   -2.68357e+05   -1.28252e+06   -1.27039e+06
>       Potential    Kinetic En.   Total Energy    Temperature Pressure (bar)
>    -2.29489e+06    3.32431e+05   -1.96246e+06    3.26740e+02    1.04578e+03
> 
> 
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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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