Hi,
I am trying to do an MD simulation of
a protein model using AMBER 12 using the following input for the equilibration
step:
------------------------------------------------------------------------------------------------
# 1st equilibration step under NPT 100000 ps
# Time-step 2 fs
&cntrl
imin=0,
irest=1,
ntx=5,
ntb=2, pres0=1.0, ntp=1, taup=2.0,
cut=9.0,
temp0=300.0,
ntc=2,
ntf=2,
ntt=3, gamma_ln=2.0, ig=-1,
nstlim=50000, dt=0.002,
ntpr=500, ntwx=500, ntwr=500,
IOUTFM=1,
IWRAP=1,
/
-----------------------------------------------------------------------------------------------------
The job is running using pmemd on a local cluster using 64 cpu. The run seemed to be OK; however,
looking at the output file I see a strange behavior. Some NSTEPs are written more than once and some are missing from the output file.
I extracted the "NSTEP" from the output (see below) and you can see that after NSTEP = 10500 ps, the program skipped NSTEP = 11000 ps
and recorded NSTEP = 11500 followed by another NSTEP = 10500 ps. The same behavior is shown for other recorded NSTEP.
The same behavior happened in the heating step but the final coordinate file seemed to be OK and the time was recorded correctly at the header.
Not sure what might be wrong with the run? Any idea what is going on?
Many thanks in advance for your help.
Thanks,
Ibrahim
--------------------------------------------------------------------------------------------------------------------
NSTEP = 500 TIME(PS) = 101.000 TEMP(K) = 299.76 PRESS = -590.7
NSTEP = 1000 TIME(PS) = 102.000 TEMP(K) = 299.82 PRESS = -547.6
NSTEP = 1500 TIME(PS) = 103.000 TEMP(K) = 299.97 PRESS = -453.5
NSTEP = 2000 TIME(PS) = 104.000 TEMP(K) = 302.06 PRESS = -451.1
NSTEP = 2500 TIME(PS) = 105.000 TEMP(K) = 300.07 PRESS = -280.7
NSTEP = 3000 TIME(PS) = 106.000 TEMP(K) = 300.41 PRESS = -183.8
NSTEP = 3500 TIME(PS) = 107.000 TEMP(K) = 301.63 PRESS = -225.2
NSTEP = 4000 TIME(PS) = 108.000 TEMP(K) = 302.24 PRESS = -151.8
NSTEP = 4500 TIME(PS) = 109.000 TEMP(K) = 300.28 PRESS = -42.8
NSTEP = 4500 TIME(PS) = 109.000 TEMP(K) = 301.30 PRESS = -281.7
NSTEP = 5000 TIME(PS) = 110.000 TEMP(K) = 300.28 PRESS = -91.7
NSTEP = 5500 TIME(PS) = 111.000 TEMP(K) = 299.76 PRESS = -117.3
NSTEP = 6000 TIME(PS) = 112.000 TEMP(K) = 299.43 PRESS = -245.3
NSTEP = 6500 TIME(PS) = 113.000 TEMP(K) = 298.03 PRESS = -239.7
NSTEP = 7500 TIME(PS) = 115.000 TEMP(K) = 300.08 PRESS = -245.9
NSTEP = 7000 TIME(PS) = 114.000 TEMP(K) = 299.07 PRESS = -224.4
NSTEP = 7500 TIME(PS) = 115.000 TEMP(K) = 299.23 PRESS = -86.7
NSTEP = 8500 TIME(PS) = 117.000 TEMP(K) = 298.98 PRESS = 197.3
NSTEP = 9000 TIME(PS) = 118.000 TEMP(K) = 301.60 PRESS = -6.6
NSTEP = 9500 TIME(PS) = 119.000 TEMP(K) = 299.59 PRESS = -116.4
NSTEP = 10000 TIME(PS) = 120.000 TEMP(K) = 300.10 PRESS = -57.5
NSTEP = 10500 TIME(PS) = 121.000 TEMP(K) = 301.66 PRESS = -180.8
NSTEP = 11500 TIME(PS) = 123.000 TEMP(K) = 300.18 PRESS = -66.8
NSTEP = 10500 TIME(PS) = 121.000 TEMP(K) = 300.49 PRESS = 114.6
NSTEP = 12000 TIME(PS) = 124.000 TEMP(K) = 301.92 PRESS = -129.1
NSTEP = 12500 TIME(PS) = 125.000 TEMP(K) = 302.06 PRESS = -110.5
NSTEP = 13500 TIME(PS) = 127.000 TEMP(K) = 300.06 PRESS = -245.1
NSTEP = 13500 TIME(PS) = 127.000 TEMP(K) = 298.56 PRESS = 0.8
NSTEP = 12500 TIME(PS) = 125.000 TEMP(K) = 301.60 PRESS = -224.0
NSTEP = 14500 TIME(PS) = 129.000 TEMP(K) = 301.24 PRESS = -163.5
NSTEP = 13500 TIME(PS) = 127.000 TEMP(K) = 299.40 PRESS = 60.2
NSTEP = 15500 TIME(PS) = 131.000 TEMP(K) = 300.66 PRESS = 217.6
NSTEP = 15500 TIME(PS) = 131.000 TEMP(K) = 301.98 PRESS = -270.6
NSTEP = 17000 TIME(PS) = 134.000 TEMP(K) = 296.77 PRESS = 45.5
NSTEP = 16500 TIME(PS) = 133.000 TEMP(K) = 299.59 PRESS = -129.1
NSTEP = 15500 TIME(PS) = 131.000 TEMP(K) = 299.86 PRESS = 130.8
NSTEP = 17500 TIME(PS) = 135.000 TEMP(K) = 299.64 PRESS = 38.8
NSTEP = 16500 TIME(PS) = 133.000 TEMP(K) = 300.35 PRESS = 38.2
NSTEP = 19000 TIME(PS) = 138.000 TEMP(K) = 299.85 PRESS = 90.7
NSTEP = 19500 TIME(PS) = 139.000 TEMP(K) = 299.00 PRESS = -49.4
NSTEP = 19500 TIME(PS) = 139.000 TEMP(K) = 301.02 PRESS = 52.0
NSTEP = 20000 TIME(PS) = 140.000 TEMP(K) = 299.10 PRESS = 88.4
NSTEP = 20500 TIME(PS) = 141.000 TEMP(K) = 299.80 PRESS = -9.9
NSTEP = 20000 TIME(PS) = 140.000 TEMP(K) = 299.84 PRESS = 235.1
NSTEP = 20500 TIME(PS) = 141.000 TEMP(K) = 298.28 PRESS = -9.2
NSTEP = 21500 TIME(PS) = 143.000 TEMP(K) = 300.84 PRESS = 85.6
NSTEP = 22500 TIME(PS) = 145.000 TEMP(K) = 299.30 PRESS = 22.8
NSTEP = 23000 TIME(PS) = 146.000 TEMP(K) = 299.13 PRESS = 25.2----------------------------------------------------------------------------------------------------------------------
Ibrahim M.Moustafa, Ph.D.
Pennsylvania State University
Biochemistry & Molecular Biology Dept.
201 Althouse Lab.
University Park, PA16802
Tel (814)863 8703
Fax (814)865 7927
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Received on Mon Nov 03 2014 - 08:00:02 PST
