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

[Sukit Leekumjorn]

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?

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