[gmx-developers] [Fwd: coulomb SR in 3.3cvs]

[Michel Cuendet]

Hi David,

No, there is no LJ-LR when runnnig g_energy. (?)

I'm using parrinello-rahman pressure coupling. But it seems to me that 
there is no significant difference related to that :

3.2.1 :

----------------------------------------------------------------

Volume                      887.289    1.27296    1.25576 -0.0555579  -0.722363
pV                         -187.347    5068.08    5066.15      37.24    484.195
Pressure (bar)             -3.46691    94.8199    94.7838   0.697585       9.07
Density (SI)                1005.13    1.44124    1.42162  0.0631539   0.821127

3.3
----------------------------------------------------------------
Volume                      887.104    1.40517    1.39327  0.0596162   0.632051
pV                          11.4915    5133.23    5129.17    66.7174    707.338
Pressure (bar)             0.282085    96.0735    95.9974    1.24973    13.2496
Density (SI)                1005.34    1.59044    1.57699 -0.0674518  -0.715124


Thanks for your assitsance !

Bye,

Michel

Below is my mdp file :


constraints         =  hbonds

integrator          =  md

dt                  =  0.002    ; ps !

nsteps              =  2000000  ; total 4.0 ns.

nstcomm             =  1

nstxout             =  20000

nstvout             =  100000

nstfout             =  0

nstlog              =  1000

nstenergy           =  10

nstxtcout           =  10

xtc_grps            =  System

nstlist             =  10

ns_type             =  grid

coulombtype         =  PME

rlist               =  1.0

rcoulomb            =  1.0

vdwtype             = shift

rvdw_switch         =  0.9

rvdw                =  1.0

Tcoupl              =  nose-hoover

tc-grps             =  Protein  Other

tau_t               =  0.1      0.1

ref_t               =  300      300

energygrps          =  T MHC_a12_Tax

Pcoupl              =  parrinello-rahman

Pcoupltype          =  isotropic

tau_p               =  1.0

compressibility     =  4.5e-5

ref_p               =  1.0



David van der Spoel wrote:

>On Mon, 18 Jul 2005, Michel Cuendet wrote:
>
>  
>
>>Hi,
>>
>>I subitted this message already on the gmx-users mailing list, but got no
>>feedback. I think it's an important issue for the CVS version 3.3. In the
>>meantime, I could reproduce the problem on xeon cpus, so it's not itanium specific.
>>    
>>
>
>Are these all the energies? No LJ-LR?
>Are you running pressure coupling? If so check differences there as well.
>
>Do also check the revisions page.
>
>  
>
>>Here is the original message :
>>--------------------------------------------------------------------------------
>>
>>I compiled the 3.3 CVS version of 27.05.2005 on itanium2 with the intel
>>8.1 compiler. (for those who don't know, the cvs version brings a
>>terrific speedup on itaniums). Tests were performed with both versions
>>in double precision.
>>
>>I compared the different energies obtained with 3.2.1 and 3.3, by taking
>>the same trr (from a 3.2.1 equilibration, 85000 atoms, PME) and running
>>it with both versions for about 12ps. From the tables below, one sees
>>that there is a gap between Coulomb (SR) of 3450 KJ/mol, and between
>>potential energies of  3280 KJ/mol.
>>
>>A close inspection of the energy files reveals that the version 3.3
>>reproduces the same energy as 3.2.1 at the first step, but the system
>>relaxes very quickly (0.5ps) to a lower energy with 3.3.
>>
>>Rerunning with 3.3 the trajectory produced by 3.2.1 surprisingly gives
>>the correct energies.
>>
>>Any explaination for that ?
>>
>>Thanks,
>>Michel
>>
>>
>>3.2.1 :
>>
>>Energy                      Average       RMSD     Fluct.      Drift  Tot-Drift
>>
>>-------------------------------------------------------------------------------
>>
>>G96Bond                      6723.8    140.873    138.612   -6.69756   -87.0817
>>
>>G96Angle                    10213.6    173.746    173.579    2.02771    26.3642
>>
>>Proper Dih.                 4446.16    89.4129    84.2042    8.01199    104.172
>>
>>Improper Dih.               3264.55     78.886    78.3318   -2.48685    -32.334
>>
>>LJ-14                       852.608     79.621      79.52     1.0681    13.8874
>>
>>Coulomb-14                  62903.9    126.041    122.079   -8.35397   -108.618
>>
>>LJ (SR)                      166906    1099.22     1099.1   -4.19132   -54.4955
>>
>>Coulomb (SR)             -1.2043e+06    1629.38    1629.34    -3.3074   -43.0028
>>
>>Coulomb (LR)                -188686     91.952    90.6651    4.08445     53.106
>>
>>Potential                -1.13768e+06    1031.78    1031.12   -9.84429   -127.995
>>
>>3.3 CVS
>>
>>Energy                      Average       RMSD     Fluct.      Drift  Tot-Drift
>>
>>-------------------------------------------------------------------------------
>>
>>G96Bond                     6486.57    122.559    120.492   -7.32269   -77.6351
>>
>>G96Angle                    10003.9    152.062    152.054  -0.496268   -5.26144
>>
>>Proper Dih.                 4391.87    83.2508    80.8574    6.47554    68.6537
>>
>>Improper Dih.               3194.22    78.6896    78.6495   0.819815    8.69168
>>
>>LJ-14                       833.553    76.0076    75.8776   -1.45206   -15.3947
>>
>>Coulomb-14                    62899    124.539     123.82   -4.36711   -46.3001
>>
>>LJ (SR)                      167720    1182.33    1157.55    78.6782    834.146
>>
>>Coulomb (SR)             -1.20775e+06    1897.76    1850.85   -137.014   -1452.62
>>
>>Coul. recip.                -188746     100.09    100.079    0.48938    5.18841
>>
>>Potential                -1.14096e+06    1149.25    1132.33   -64.1897   -680.539
>>
>>
>>
>>    
>>
>
>  
>

-- 
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Michel Cuendet, Ph.D. student
Laboratory of Computational Biochemistry and Chemistry
Swiss Federal Institute of Technology in Lausanne (EPFL)
CH-1015 Lausanne						
Switzerland                            Phone : +41 21 693 0324
lcbcpc21.epfl.ch/~mitch	                       +41  1 633 4194
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++