Dear AMBER users
I want to extract a low energy from summary.EPTOT
perl process_mdout.perl my_md.out
cat summary.EPTOT | awk '{if($2<min) {min=$2;print $1" "min}}'
300.000 -33775.7478
301.000 -33915.4502
303.000 -33955.8453
304.000 -34109.9068
355.000 -34114.5209
378.000 -34165.6668
*437.000 -34194.4972*
the I have used following command
VINCE.MARIE-PC:analysis$ grep 437.000 ../CL112_ZAFF_solvate_md.out
Output
ENERGY
*NSTEP = 137000 TIME(PS) = 437.000 TEMP(K) = 301.24 PRESS
= 0.0* *-34194.4972*
NSTEP = 1137000 TIME(PS) = 1437.000 TEMP(K) = 302.92 PRESS =
0.0 -33999.5303
NSTEP = 2137000 TIME(PS) = 2437.000 TEMP(K) = 299.31 PRESS =
0.0 -33798.9514
NSTEP = 3137000 TIME(PS) = 3437.000 TEMP(K) = 301.66 PRESS =
0.0 -33927.8509
NSTEP = 4137000 TIME(PS) = 4437.000 TEMP(K) = 298.71 PRESS =
0.0 -33635.1956
NSTEP = 4370000 TIME(PS) = 4670.000 TEMP(K) = 301.44 PRESS =
0.0 -33802.0443
NSTEP = 4371000 TIME(PS) = 4671.000 TEMP(K) = 305.06 PRESS =
0.0 -33796.4854
NSTEP = 4372000 TIME(PS) = 4672.000 TEMP(K) = 298.73 PRESS =
0.0 -33652.5826
NSTEP = 4373000 TIME(PS) = 4673.000 TEMP(K) = 302.32 PRESS =
0.0 -33654.1411
NSTEP = 4374000 TIME(PS) = 4674.000 TEMP(K) = 302.53 PRESS =
0.0 -33761.5785
NSTEP = 4375000 TIME(PS) = 4675.000 TEMP(K) = 303.29 PRESS =
0.0 -33652.0619
NSTEP = 4376000 TIME(PS) = 4676.000 TEMP(K) = 306.41 PRESS =
0.0 -33767.6697
NSTEP = 4377000 TIME(PS) = 4677.000 TEMP(K) = 301.57 PRESS =
0.0 -33769.6163
NSTEP = 4378000 TIME(PS) = 4678.000 TEMP(K) = 297.86 PRESS =
0.0 -33772.0896
NSTEP = 4379000 TIME(PS) = 4679.000 TEMP(K) = 297.98 PRESS =
0.0 -33678.0282
NSTEP = 5137000 TIME(PS) = 5437.000 TEMP(K) = 299.61 PRESS =
0.0 -33681.4740
NSTEP = 6137000 TIME(PS) = 6437.000 TEMP(K) = 304.40 PRESS =
0.0 -33673.9064
NSTEP = 7137000 TIME(PS) = 7437.000 TEMP(K) = 300.80 PRESS =
0.0 -33654.2776
NSTEP = 8137000 TIME(PS) = 8437.000 TEMP(K) = 292.55 PRESS =
0.0 -33608.0894
NSTEP = 9137000 TIME(PS) = 9437.000 TEMP(K) = 300.61 PRESS =
0.0 *-33667.9165*
VINCE.MARIE-PC:analysis$
For the low energy frame 137000/1000(ntwx)=137 frames, that is very
beginning of 10 ns MD simulation at 300K.
My question is for this command "VINCE.MARIE-PC:analysis$ grep 437.000
../CL112_ZAFF_solvate_md.out " why it out puts
many options, is it possible to even consider other "nsteps" to extract
lower energy structure. I have found that 137000/1000=137 frames
looses its folding but "nsteps 9137000/1000=9137" frame has maintained
expected folding. The energy of the frames from the end of MD simulation
is little higher then the initial frame, I didn't under stand why in the
output file I have many possibilities? i.e 437.000 at different "ps" time.
thanks in advance..
VINCE
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Received on Fri Mar 11 2016 - 01:30:04 PST
