From: Jiyong Park (jiyong_at_mbi.ucla.edu)
Date: Fri Aug 03 2012 - 17:48:42 CDT
Dear NAMDers
I'm wondering if accelerated MD (aMD)
module in NAMD v2.9 is compliant with
GPU acceleration. As I turned on dual
boost mode (aMDdual), 100 Angstrom cubic
simulation box blows away after 1 ns.
Also aMD output was found strange, as
'POTENTIAL' term gives strange numbers
as shown below.
Jiyong
ACCELERATED MD: STEP 82500 dV 0 dVAVG 14.8469 BOND 1030.51 ANGLE 2942.5
DIHED 1895.19 IMPRP 197.105 ELECT -1.53329e+06 VDW 0 POTENTIAL -1.52723e
+06
ACCELERATED MD: STEP 83000 dV 0 dVAVG 14.8269 BOND 1047.4 ANGLE 2983.64
DIHED 1866.04 IMPRP 193.489 ELECT -1.53329e+06 VDW 0 POTENTIAL -1.5272e
+06
ACCELERATED MD: STEP 83500 dV 40.4412 dVAVG 14.5098 BOND 1049.59 ANGLE
2933.46 DIHED 1801.26 IMPRP 190.028 ELECT -1.53327e+06 VDW 0 POTENTIAL
-1.52729e+06
ACCELERATED MD: STEP 84000 dV 15.2513 dVAVG 16.722 BOND 1078.75 ANGLE
2994.91 DIHED 1827.86 IMPRP 190.737 ELECT -19489.6 VDW -3696.06
POTENTIAL -17093.4
ACCELERATED MD: STEP 84500 dV 72.5276 dVAVG 11.7537 BOND 1051.42 ANGLE
2993.8 DIHED 1768.57 IMPRP 184.95 ELECT -1.53331e+06 VDW 0 POTENTIAL
-1.52731e+06
ACCELERATED MD: STEP 85000 dV 36.1124 dVAVG 10.2101 BOND 1039.06 ANGLE
2942.09 DIHED 1805.73 IMPRP 186.164 ELECT -1.53331e+06 VDW 0 POTENTIAL
-1.52734e+06
ACCELERATED MD: STEP 85500 dV 35.0806 dVAVG 16.5325 BOND 1076.04 ANGLE
2965.07 DIHED 1806.8 IMPRP 186.546 ELECT -1.53329e+06 VDW 0 POTENTIAL
-1.52725e+06
ACCELERATED MD: STEP 86000 dV 3.93079 dVAVG 12.9962 BOND 1115.8 ANGLE
2946.98 DIHED 1841.46 IMPRP 184.416 ELECT -1.53328e+06 VDW 0 POTENTIAL
-1.52719e+06
ACCELERATED MD: STEP 86500 dV 0 dVAVG 10.0645 BOND 1070.48 ANGLE 3001.53
DIHED 1877.92 IMPRP 185.192 ELECT -1.5333e+06 VDW 0 POTENTIAL -1.52716e
+06
ACCELERATED MD: STEP 87000 dV 0.0296667 dVAVG 9.87065 BOND 1068 ANGLE
2892.31 DIHED 1849.44 IMPRP 176.198 ELECT -1.53328e+06 VDW 0 POTENTIAL
-1.52729e+06
ACCELERATED MD: STEP 87500 dV 10.4681 dVAVG 14.1485 BOND 1054.6 ANGLE
2958.91 DIHED 1833.27 IMPRP 202.112 ELECT -1.53326e+06 VDW 0 POTENTIAL
-1.52721e+06
ACCELERATED MD: STEP 88000 dV 0.269308 dVAVG 12.6524 BOND 1054.08 ANGLE
2931.54 DIHED 1848.22 IMPRP 186.06 ELECT -19501.3 VDW -3714.77 POTENTIAL
-17196.2
ACCELERATED MD: STEP 88500 dV 55.5354 dVAVG 14.8164 BOND 1055.58 ANGLE
3036.97 DIHED 1785.81 IMPRP 185.722 ELECT -1.53327e+06 VDW 0 POTENTIAL
-1.5272e+06
ACCELERATED MD: STEP 89000 dV 39.1479 dVAVG 11.5679 BOND 1027.7 ANGLE
3038.08 DIHED 1802.59 IMPRP 170.527 ELECT -1.53329e+06 VDW 0 POTENTIAL
-1.52725e+06
ACCELERATED MD: STEP 89500 dV 0 dVAVG 12.81 BOND 1097.56 ANGLE 2920.78
DIHED 1873.2 IMPRP 201.45 ELECT -1.53329e+06 VDW 0 POTENTIAL -1.5272e+06
-- Jiyong Park Postdoctoral Research Associate Dept. of Chemistry and Biochemistry Univ. California, Los Angeles Email: jiyong_at_mbi.ucla.edu
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