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

[Michel Cuendet]

Hi guys,

Are there any news about that issue (see below my original message to this list)?

I've been trying to figure out what could in theory cause a relaxation of the 
coulomb SR energy in 3.3.a lower than in 3.2.1. It could be something with the 
constraints (I constrain all bonds involving hydrogens) ?

By minimizing with 321 and subsequently with 33a, I see the same kind of energy 
difference as reported below. But there is no big apprarent movement. RMSD's 
between the two conformations are of the order of 0.0005 nm for the protein, and 
0.0015 for the water, uniformly spread over atom numbers except for a few 
molecules jumping the cell boundary...

I would really like to know if 3.3.a is usable or not...

Thanks to anyone commenting on that issue,

Michel


-------- Original Message --------
Subject: coulomb SR in 3.3cvs
Date: Mon, 11 Jul 2005 17:34:42 +0200
From: Michel Cuendet <michel.cuendet at epfl.ch>
Reply-To: michel.cuendet at epfl.ch
To: gmx-users at gromacs.org
References: <20050711100013.A17C62509A at xray.bmc.uu.se>

Hi,

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, and were reproduced on an athlon platform.

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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++