From: Xiaoqing Wang (kitty_wxq_at_yahoo.com.cn)
Date: Tue May 10 2005 - 07:31:31 CDT
Dear all,
We have recently started to use NAMD to run macromolecular simulations.
NAMD is a powerful and user-friendly software, and we really like it.
I have compiled charm++/namd on amd64.
"./build charm++ mpi-linux opteron -no-build-shared" when build charm
I downloaded binary namd "NAMD_2.5_Linux-i686" on my own intel P4 CPU.
But when I run the same program with the same input files on the
different cpus, the results are different.
The attachment file "equil.namd" is input file.
The attachment file "equil_out2.xst" is from intel cpu and
"equil_out2_amd64.xst" is from amd64 when I use 1 cpu.
My system become larger when equilibrate the system on amd64.
Any more files needed?
Any tips would be greatly appreciated!
Sincerely,
Xiaoqing
# NAMD extended system trajectory file
#$LABELS step a_x a_y a_z b_x b_y b_z c_x c_y c_z o_x o_y o_z
2000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
3000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
4000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
5000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
6000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
7000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
8000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
9000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
10000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
11000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
12000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
13000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
14000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
15000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
16000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
17000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
18000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
19000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
20000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
21000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
22000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
22000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739 0 0 0 0 0 0
23000 101.202 0 0 0 98.9957 0 0 0 82.9164 2.94 2.574 2.739 -1.77144e-06 -1.77144e-06 -1.77144e-06 0 0 0
24000 100.53 0 0 0 98.3383 0 0 0 82.3658 2.94 2.574 2.739 1.95836e-05 1.95836e-05 1.95836e-05 0 0 0
25000 100.056 0 0 0 97.8745 0 0 0 81.9774 2.94 2.574 2.739 -1.50124e-05 -1.50124e-05 -1.50124e-05 0 0 0
26000 99.6187 0 0 0 97.447 0 0 0 81.6193 2.94 2.574 2.739 3.13283e-05 3.13283e-05 3.13283e-05 0 0 0
27000 99.4364 0 0 0 97.2687 0 0 0 81.47 2.94 2.574 2.739 2.31009e-05 2.31009e-05 2.31009e-05 0 0 0
28000 99.1887 0 0 0 97.0264 0 0 0 81.267 2.94 2.574 2.739 1.0417e-05 1.0417e-05 1.0417e-05 0 0 0
29000 98.995 0 0 0 96.837 0 0 0 81.1084 2.94 2.574 2.739 -1.53184e-05 -1.53184e-05 -1.53184e-05 0 0 0
30000 98.7833 0 0 0 96.6298 0 0 0 80.9349 2.94 2.574 2.739 -1.89625e-05 -1.89625e-05 -1.89625e-05 0 0 0
31000 98.5904 0 0 0 96.4411 0 0 0 80.7768 2.94 2.574 2.739 1.75072e-06 1.75072e-06 1.75072e-06 0 0 0
32000 98.4983 0 0 0 96.3511 0 0 0 80.7014 2.94 2.574 2.739 -7.4191e-06 -7.4191e-06 -7.4191e-06 0 0 0
33000 98.3912 0 0 0 96.2463 0 0 0 80.6136 2.94 2.574 2.739 -1.4581e-06 -1.4581e-06 -1.4581e-06 0 0 0
34000 98.312 0 0 0 96.1688 0 0 0 80.5487 2.94 2.574 2.739 1.17994e-05 1.17994e-05 1.17994e-05 0 0 0
35000 98.2029 0 0 0 96.0621 0 0 0 80.4593 2.94 2.574 2.739 -1.52594e-05 -1.52594e-05 -1.52594e-05 0 0 0
36000 98.1086 0 0 0 95.9698 0 0 0 80.3821 2.94 2.574 2.739 2.75658e-05 2.75658e-05 2.75658e-05 0 0 0
37000 98.0597 0 0 0 95.922 0 0 0 80.342 2.94 2.574 2.739 -1.0722e-05 -1.0722e-05 -1.0722e-05 0 0 0
38000 98.018 0 0 0 95.8812 0 0 0 80.3078 2.94 2.574 2.739 -1.48343e-05 -1.48343e-05 -1.48343e-05 0 0 0
39000 97.9615 0 0 0 95.826 0 0 0 80.2616 2.94 2.574 2.739 -9.93629e-06 -9.93629e-06 -9.93629e-06 0 0 0
40000 97.7832 0 0 0 95.6516 0 0 0 80.1155 2.94 2.574 2.739 6.52457e-06 6.52457e-06 6.52457e-06 0 0 0
41000 97.775 0 0 0 95.6435 0 0 0 80.1087 2.94 2.574 2.739 3.63865e-06 3.63865e-06 3.63865e-06 0 0 0
42000 97.7198 0 0 0 95.5896 0 0 0 80.0636 2.94 2.574 2.739 -1.15336e-05 -1.15336e-05 -1.15336e-05 0 0 0
42000 97.7198 0 0 0 95.5896 0 0 0 80.0636 2.94 2.574 2.739 -1.15336e-05 -1.15336e-05 -1.15336e-05 0 0 0
# NAMD extended system trajectory file
#$LABELS step a_x a_y a_z b_x b_y b_z c_x c_y c_z o_x o_y o_z
2000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
3000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
4000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
5000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
6000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
7000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
8000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
9000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
10000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
11000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
12000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
13000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
14000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
15000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
16000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
17000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
18000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
19000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
20000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
21000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
22000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
22000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739 0 0 0 0 0 0
23000 101.202 0 0 0 98.9957 0 0 0 82.9164 2.94 2.574 2.739 -1.77144e-06 -1.77144e-06 -1.77144e-06 0 0 0
24000 100.53 0 0 0 98.3383 0 0 0 82.3658 2.94 2.574 2.739 1.95836e-05 1.95836e-05 1.95836e-05 0 0 0
25000 100.056 0 0 0 97.8745 0 0 0 81.9774 2.94 2.574 2.739 -1.50124e-05 -1.50124e-05 -1.50124e-05 0 0 0
26000 99.6187 0 0 0 97.447 0 0 0 81.6193 2.94 2.574 2.739 3.13283e-05 3.13283e-05 3.13283e-05 0 0 0
27000 99.4364 0 0 0 97.2687 0 0 0 81.47 2.94 2.574 2.739 2.31009e-05 2.31009e-05 2.31009e-05 0 0 0
28000 99.1887 0 0 0 97.0264 0 0 0 81.267 2.94 2.574 2.739 1.0417e-05 1.0417e-05 1.0417e-05 0 0 0
29000 98.995 0 0 0 96.837 0 0 0 81.1084 2.94 2.574 2.739 -1.53184e-05 -1.53184e-05 -1.53184e-05 0 0 0
30000 98.7833 0 0 0 96.6298 0 0 0 80.9349 2.94 2.574 2.739 -1.89625e-05 -1.89625e-05 -1.89625e-05 0 0 0
31000 98.5904 0 0 0 96.4411 0 0 0 80.7768 2.94 2.574 2.739 1.75072e-06 1.75072e-06 1.75072e-06 0 0 0
32000 98.4983 0 0 0 96.3511 0 0 0 80.7014 2.94 2.574 2.739 -7.4191e-06 -7.4191e-06 -7.4191e-06 0 0 0
33000 98.3912 0 0 0 96.2463 0 0 0 80.6136 2.94 2.574 2.739 -1.4581e-06 -1.4581e-06 -1.4581e-06 0 0 0
34000 98.312 0 0 0 96.1688 0 0 0 80.5487 2.94 2.574 2.739 1.17994e-05 1.17994e-05 1.17994e-05 0 0 0
35000 98.2029 0 0 0 96.0621 0 0 0 80.4593 2.94 2.574 2.739 -1.52594e-05 -1.52594e-05 -1.52594e-05 0 0 0
36000 98.1086 0 0 0 95.9698 0 0 0 80.3821 2.94 2.574 2.739 2.75658e-05 2.75658e-05 2.75658e-05 0 0 0
37000 98.0597 0 0 0 95.922 0 0 0 80.342 2.94 2.574 2.739 -1.0722e-05 -1.0722e-05 -1.0722e-05 0 0 0
38000 98.018 0 0 0 95.8812 0 0 0 80.3078 2.94 2.574 2.739 -1.48343e-05 -1.48343e-05 -1.48343e-05 0 0 0
39000 97.9615 0 0 0 95.826 0 0 0 80.2616 2.94 2.574 2.739 -9.93629e-06 -9.93629e-06 -9.93629e-06 0 0 0
40000 97.7832 0 0 0 95.6516 0 0 0 80.1155 2.94 2.574 2.739 6.52457e-06 6.52457e-06 6.52457e-06 0 0 0
41000 97.775 0 0 0 95.6435 0 0 0 80.1087 2.94 2.574 2.739 3.63865e-06 3.63865e-06 3.63865e-06 0 0 0
42000 97.7198 0 0 0 95.5896 0 0 0 80.0636 2.94 2.574 2.739 -1.15336e-05 -1.15336e-05 -1.15336e-05 0 0 0
42000 97.7198 0 0 0 95.5896 0 0 0 80.0636 2.94 2.574 2.739 -1.15336e-05 -1.15336e-05 -1.15336e-05 0 0 0
# NAMD extended system trajectory file
#$LABELS step a_x a_y a_z b_x b_y b_z c_x c_y c_z o_x o_y o_z
2000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
3000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
4000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
5000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
6000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
7000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
8000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
9000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
10000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
11000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
12000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
13000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
14000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
15000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
16000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
17000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
18000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
19000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
20000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
21000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
22000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739
22000 103.12 0 0 0 100.872 0 0 0 84.488 2.94 2.574 2.739 0 0 0 0 0 0
23000 114.142 0 0 0 111.654 0 0 0 93.5188 2.94 2.574 2.739 7.61067e-05 7.61067e-05 7.61067e-05 0 0 0
24000 121.194 0 0 0 118.552 0 0 0 99.2964 2.94 2.574 2.739 7.93349e-05 7.93349e-05 7.93349e-05 0 0 0
25000 128.623 0 0 0 125.819 0 0 0 105.383 2.94 2.574 2.739 8.89362e-05 8.89362e-05 8.89362e-05 0 0 0
26000 136.231 0 0 0 133.261 0 0 0 111.617 2.94 2.574 2.739 3.83094e-05 3.83094e-05 3.83094e-05 0 0 0
27000 144.784 0 0 0 141.628 0 0 0 118.624 2.94 2.574 2.739 7.86805e-05 7.86805e-05 7.86805e-05 0 0 0
28000 153.658 0 0 0 150.308 0 0 0 125.895 2.94 2.574 2.739 8.35225e-05 8.35225e-05 8.35225e-05 0 0 0
29000 163.274 0 0 0 159.714 0 0 0 133.773 2.94 2.574 2.739 5.86213e-05 5.86213e-05 5.86213e-05 0 0 0
30000 173.552 0 0 0 169.769 0 0 0 142.194 2.94 2.574 2.739 7.20347e-05 7.20347e-05 7.20347e-05 0 0 0
31000 184.194 0 0 0 180.178 0 0 0 150.913 2.94 2.574 2.739 8.17792e-05 8.17792e-05 8.17792e-05 0 0 0
32000 195.654 0 0 0 191.389 0 0 0 160.303 2.94 2.574 2.739 4.17505e-05 4.17505e-05 4.17505e-05 0 0 0
33000 207.741 0 0 0 203.212 0 0 0 170.206 2.94 2.574 2.739 4.43198e-05 4.43198e-05 4.43198e-05 0 0 0
34000 220.691 0 0 0 215.88 0 0 0 180.816 2.94 2.574 2.739 6.31962e-05 6.31962e-05 6.31962e-05 0 0 0
35000 234.848 0 0 0 229.728 0 0 0 192.415 2.94 2.574 2.739 4.05792e-05 4.05792e-05 4.05792e-05 0 0 0
36000 249.282 0 0 0 243.848 0 0 0 204.241 2.94 2.574 2.739 6.72314e-05 6.72314e-05 6.72314e-05 0 0 0
37000 264.646 0 0 0 258.877 0 0 0 216.829 2.94 2.574 2.739 8.63443e-05 8.63443e-05 8.63443e-05 0 0 0
38000 281.755 0 0 0 275.613 0 0 0 230.847 2.94 2.574 2.739 3.6956e-05 3.6956e-05 3.6956e-05 0 0 0
39000 300.301 0 0 0 293.754 0 0 0 246.042 2.94 2.574 2.739 5.65007e-05 5.65007e-05 5.65007e-05 0 0 0
40000 319.358 0 0 0 312.396 0 0 0 261.655 2.94 2.574 2.739 5.05448e-05 5.05448e-05 5.05448e-05 0 0 0
41000 340.374 0 0 0 332.954 0 0 0 278.875 2.94 2.574 2.739 6.83717e-05 6.83717e-05 6.83717e-05 0 0 0
42000 362.326 0 0 0 354.428 0 0 0 296.86 2.94 2.574 2.739 4.60951e-05 4.60951e-05 4.60951e-05 0 0 0
42000 362.326 0 0 0 354.428 0 0 0 296.86 2.94 2.574 2.739 4.60951e-05 4.60951e-05 4.60951e-05 0 0 0
43000 531.572 0 0 0 519.984 0 0 0 435.526 2.94 2.574 2.739 0.000350383 0.000350383 0.000350383 0 0 0
44000 719.408 0 0 0 703.725 0 0 0 589.424 2.94 2.574 2.739 0.000211825 0.000211825 0.000211825 0 0 0
45000 843.195 0 0 0 824.813 0 0 0 690.844 2.94 2.574 2.739 0.000120186 0.000120186 0.000120186 0 0 0
46000 914.453 0 0 0 894.518 0 0 0 749.227 2.94 2.574 2.739 0.000113972 0.000113972 0.000113972 0 0 0
47000 970.209 0 0 0 949.058 0 0 0 794.909 2.94 2.574 2.739 5.37219e-05 5.37219e-05 5.37219e-05 0 0 0
48000 1021.23 0 0 0 998.972 0 0 0 836.715 2.94 2.574 2.739 3.53288e-05 3.53288e-05 3.53288e-05 0 0 0
49000 1067.71 0 0 0 1044.43 0 0 0 874.792 2.94 2.574 2.739 4.82713e-05 4.82713e-05 4.82713e-05 0 0 0
50000 1112.04 0 0 0 1087.8 0 0 0 911.117 2.94 2.574 2.739 6.23223e-05 6.23223e-05 6.23223e-05 0 0 0
51000 1149.85 0 0 0 1124.79 0 0 0 942.096 2.94 2.574 2.739 3.10368e-05 3.10368e-05 3.10368e-05 0 0 0
52000 1192.28 0 0 0 1166.29 0 0 0 976.855 2.94 2.574 2.739 2.7736e-05 2.7736e-05 2.7736e-05 0 0 0
53000 1229.58 0 0 0 1202.78 0 0 0 1007.42 2.94 2.574 2.739 4.31892e-05 4.31892e-05 4.31892e-05 0 0 0
54000 1258.8 0 0 0 1231.36 0 0 0 1031.36 2.94 2.574 2.739 3.64121e-05 3.64121e-05 3.64121e-05 0 0 0
55000 1293.76 0 0 0 1265.56 0 0 0 1060 2.94 2.574 2.739 9.0032e-06 9.0032e-06 9.0032e-06 0 0 0
56000 1324.32 0 0 0 1295.45 0 0 0 1085.04 2.94 2.574 2.739 4.81977e-05 4.81977e-05 4.81977e-05 0 0 0
57000 1352.81 0 0 0 1323.31 0 0 0 1108.38 2.94 2.574 2.739 2.3104e-05 2.3104e-05 2.3104e-05 0 0 0
58000 1378.95 0 0 0 1348.89 0 0 0 1129.8 2.94 2.574 2.739 2.23174e-05 2.23174e-05 2.23174e-05 0 0 0
59000 1404.51 0 0 0 1373.89 0 0 0 1150.74 2.94 2.574 2.739 5.2084e-06 5.2084e-06 5.2084e-06 0 0 0
60000 1429.29 0 0 0 1398.13 0 0 0 1171.04 2.94 2.574 2.739 1.0399e-05 1.0399e-05 1.0399e-05 0 0 0
61000 1451 0 0 0 1419.37 0 0 0 1188.83 2.94 2.574 2.739 5.31657e-06 5.31657e-06 5.31657e-06 0 0 0
62000 1469.66 0 0 0 1437.62 0 0 0 1204.12 2.94 2.574 2.739 2.01754e-05 2.01754e-05 2.01754e-05 0 0 0
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