[gmx-users] compare 3.3.3 vs 3.99.4 (bit long)
spitaleri.andrea at hsr.it
spitaleri.andrea at hsr.it
Thu Aug 28 14:18:28 CEST 2008
Dear all,
I am using the Louhi cluster on the Finnish IT center
(http://www.csc.fi/english) and I had the chance to test the latest beta
version of gromacs (3.99.4). First of all I have to say that it is very
fast and very scalable. Now, reliability. I have run a 2ns simulation of
a protein in water (ca. 200,000 atoms) using 3.3.3 and 3.99.4 and 2 fs
integration time.
Our home cluster (ibm intel 2.66 Ghz) bearing 3.3.3 needs about 4d for
2ns on 24 nodes, whereas louhi with 3.99.4 on 64 nodes needs about 15h!
good stuff.
I have checked the energies for both simulation and below you see the
results:
######
3.99.4
######
Statistics over 1000001 steps [ 0.0000 thru 2000.0001 ps ], 27 data sets
Energy Average RMSD Fluct. Drift
Tot-Drift
-------------------------------------------------------------------------------
Angle 46984.2 307.076 298.32 -0.126109
-252.218
Proper Dih. 2743.89 67.4457 66.9484 -0.01416
-28.32
Ryckaert-Bell. 20897.7 387.982 219.399 -0.554239
-1108.48
LJ-14 33023.1 136.292 135.93 0.0171902
34.3805
Coulomb-14 148467 195.67 194.323 -0.0396933
-79.3867
LJ (SR) 538656 1748.75 1747.19 -0.128059
-256.119
Coulomb (SR) -4.0367e+06 2448.62 2428.54 -0.542011
-1084.02
Coul. recip. -865148 242.753 242.316 -0.0252178
-50.4356
Potential -4.11107e+06 1663.33 1449.76 -1.4123
-2824.61
Kinetic En. 772334 983.851 983.705 0.0293455
58.691
Total Energy -3.33874e+06 1346.81 1084.61 -1.38295
-2765.91
Temperature 299.984 0.38214 0.382083 1.13975e-05
0.0227951
Pressure (bar) 1.15551 37.5452 37.5448 0.000308348
0.616696
Volume 3153.75 1.38233 1.3728 -0.000280674
-0.561349
Density (SI) 994.349 0.435839 0.432836 8.84706e-05
0.176941
Coul-SR:Protein-Protein -67091 453.617 453.564 0.0119892
23.9785
LJ-SR:Protein-Protein -43707.5 234.515 205.403 -0.196011
-392.022
Coul-14:Protein-Protein 148185 195.603 194.174 -0.0408786
-81.7573
LJ-14:Protein-Protein 32996.1 136.26 135.868 0.0178968
35.7937
Coul-SR:Protein-Other -116084 1057.65 1025.74 -0.446636
-893.273
LJ-SR:Protein-Other -6113.29 324.853 321.225 0.0838503
167.701
Coul-14:Protein-Other 18.5116 3.66015 3.16015 -0.0031985
-6.39701
LJ-14:Protein-Other 16.2657 3.3305 3.31851 0.000489169
0.978339
Coul-SR:Other-Other -3.85352e+06 2476.7 2475.92 -0.107357
-214.713
LJ-SR:Other-Other 588476 1731.91 1731.88 -0.0158981
-31.7962
Coul-14:Other-Other 263.365 6.86274 6.37901 0.00438365
8.7673
LJ-14:Other-Other 10.752 3.07146 2.99287 -0.00119576
-2.39153
Heat Capacity Cv: 12.4718 J/mol K (factor = 1.62274e-06)
Isothermal Compressibility: 1.46289e-05 /bar
Adiabatic bulk modulus: 68357.7 bar
#####
3.3.3
#####
Statistics over 1000001 steps [ 0.0000 thru 2000.0001 ps ], 27 data sets
Energy Average RMSD Fluct. Drift
Tot-Drift
-------------------------------------------------------------------------------
Angle 46944.4 319.789 295.167 -0.21313
-426.26
Proper Dih. 2755.63 69.3266 66.9131 -0.0314078
-62.8156
Ryckaert-Bell. 20953.3 374.694 221.951 -0.522876
-1045.75
LJ-14 33118.6 140.075 137.154 0.0492889
98.5779
Coulomb-14 148701 188.693 187.295 -0.0397171
-79.4343
LJ (SR) 538555 1749.63 1748.67 -0.100002
-200.004
Coulomb (SR) -4.03654e+06 2470.23 2458.61 -0.414596
-829.193
Coul. recip. -865451 236.417 235.938 -0.0260338
-52.0677
Potential -4.11096e+06 1656.99 1477.7 -1.29848
-2596.96
Kinetic En. 772333 984.094 983.984 -0.0254802
-50.9604
Total Energy -3.33863e+06 1338 1098.16 -1.32396
-2647.92
Temperature 299.984 0.382234 0.382192 -9.89665e-06
-0.0197933
Pressure (bar) 1.01847 37.5027 37.4954 0.0012831
2.5662
Volume 3154.08 1.45018 1.44809 -0.000134813
-0.269625
Density (SI) 994.246 0.457148 0.456488 4.25118e-05
0.0850236
Coul-SR:Protein-Protein -67562.2 390.93 384.643 0.12095
241.9
LJ-SR:Protein-Protein -43829.4 268.207 216.54 -0.27411
-548.22
Coul-14:Protein-Protein 148701 188.693 187.295 -0.0397171
-79.4343
LJ-14:Protein-Protein 33118.6 140.075 137.154 0.0492889
98.5779
Coul-SR:Protein-Other -115824 993.994 877.644 -0.808267
-1616.54
LJ-SR:Protein-Other -6070.4 367.068 343.991 0.221871
443.742
Coul-14:Protein-Other 0 0 0 0
0
LJ-14:Protein-Other 0 0 0 0
0
Coul-SR:Other-Other -3.85315e+06 2483.91 2478.92 0.272709
545.419
LJ-SR:Other-Other 588455 1731.91 1731.69 -0.0477627
-95.5255
Coul-14:Other-Other 0 0 0 0
0
LJ-14:Other-Other 0 0 0 0
0
Heat Capacity Cv: 12.4718 J/mol K (factor = 1.62354e-06)
Isothermal Compressibility: 1.60985e-05 /bar
Adiabatic bulk modulus: 62117.6 bar
A first look shows that the two simulation gives similar energy results
(except for the 14 interaction protein-other and other-other).
I am thinking to use the new gmx to produce my simulation since it seems
stable enough. Any suggestion in this stage are very welcome.
thanks in advance and sorry for the long post.
Regards,
Andrea
Andrea Spitaleri PhD
Dulbecco Telethon Institute
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
Tel: 0039-0226434348/5622/3497/4922
Fax: 0039-0226434153
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