From: A D (boltzmanndist_at_yahoo.com)
Date: Wed Nov 18 2009 - 18:18:37 CST
Hi
I just recognized a little bug while running namd dynamics. I make the program write PBC every 50 steps, but the xst file is not writing #$LABELS step a_x a_y a_z b_x b_y b_z c_x c_y c_z o_x o_y o_z s_x s_y s_z s_u s_v s_w for each PBC at every line. The step number sometimes does not start at a new line. I know this is kind of unimportant, but i wanted to let people know :).
Thanks.
Here is the xst file. Things are smooth until step 200, i.e. 1 line per step, but then somehow stepnumber 250 is appended to a previous number.
# NAMD extended system trajectory file
#$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 s_x s_y s_z s_u s_v s_w
0 46.774 0 0 0 66.056 0 0 0 90.701 0 0 0 0 0 0 0 0 0
50 46.7759 0 0 0 66.0587 0 0 0 90.7362 0 0 0 6.17051e-05 6.17051e-05 -3.7901e-05 0 0 0
100 46.454 0 0 0 65.6041 0 0 0 90.2473 0 0 0 -5.31678e-05 -5.31678e-05 0.000150304 0 0 0
150 46.2843 0 0 0 65.3645 0 0 0 90.2107 0 0 0 -0.000122372 -0.000122372 -0.000109527 0 0 0
200 46.2268 0 0 0 65.2832 0 0 0 90.1288 0 0 0 -2.12269e-05 -2.12269e-05 1.33111e-06 0 0 02250 46.211 0 0 0 65.261 0 0 0 89.987 0 0 0 4.8811e-05 4.8811e-05 7.65505e-06 0 0 03300 46.2836 0 0 0 65.3634 0 0 0 89.8432 0 0 0 4.60883e-05 4.60883e-05 -6.05736e-05 0 0 03350 46.3252 0 0 0 65.4222 0 0 0 89.7252 0 0 0 -2.71445e-05 -2.71445e-05 2.40777e-05 0 0 04400 46.2904 0 0 0 65.373 0 0 0 89.7192 0 0 0 1.42747e-05 1.42747e-05 -3.07368e-05 0 0 04450 46.2442 0 0 0 65.3077 0 0 0 89.7791 0 0 0 1.35548e-05 1.35548e-05 -2.89223e-05 0 0 05500 46.2792 0 0 0 65.3572 0 0 0 89.6868 0 0 0 -3.33428e-05 -3.33428e-05 4.93795e-06 0 0 05550 46.3273 0 0 0 65.4251 0 0 0 89.7079 0 0 0 -4.40295e-05 -4.40295e-05 2.77558e-05 0 0 06600 46.2902 0 0 0 65.3727 0 0 0 89.8362 0 0 0 4.14805e-05 4.14805e-05 5.81529e-05 0 0 06650 46.3004 0 0 0 65.3872 0 0 0 89.6967 0 0 0 5.78564e-06 5.78564e-06 -4.37526e-05 0 0 07700 46.3629 00 0 65.4754 0 0 0 89.5606 0 0 0 -5.33053e-05 -5.33053e-05 -1.2982e-05
0 0 0
750 46.3528 0 0 0 65.4612 0 0 0 89.5951 0 0 0 -4.1791e-06 -4.1791e-06 3.4852e-06 0 0 0
800 46.3255 0 0 0 65.4225 0 0 0 89.5184 0 0 0 5.96176e-05 5.96176e-05 -1.1601e-05 0 0 0
850 46.4191 0 0 0 65.5548 0 0 0 89.4328 0 0 0 -9.77651e-06 -9.77651e-06 -6.33253e-05 0 0 0
900 46.373 0 0 0 65.4896 0 0 0 89.3609 0 0 0 -1.64822e-05 -1.64822e-05 3.53064e-05 0 0 0
950 46.3544 0 0 0 65.4634 0 0 0 89.4956 0 0 0 1.85604e-06 1.85604e-06 2.55426e-05 0 0 011000 46.3249 0 0 0 65.4217 0 0 0 89.5116 0 0 0 -4.23895e-05 -4.23895e-05 8.48554e-05 0 0 011050 46.2743 0 0 0 65.3504 0 0 0 89.5743 0 0 0 -8.4774e-06 -8.4774e-06 -3.04105e-05 0 0 0
1100 46.2574 0 0 0 65.3264 0 0 0 89.7702 0 0 0 -5.80695e-05 -5.80695e-05 -2.39703e-06 0 0 011150 46.2043 0 0 0 65.2514 0 0 0 89.873 0 0 0 4.8039e-05 4.8039e-05 2.17983e-05 0 0 0
0
0 0 0
1200 46.2524 0 0 0 65.3194 0 0 0 89.9263 0 0 0 2.28809e-05 2.28809e-05 -1.8444e-05 0 0 0
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