Hi Ibrahim,
That is the behavior observed when you are running more than one job at
the same time, writing to the same files.
Please check on that.
adrian
On 11/3/14 10:52 AM, IBRAHIM M ABDELRADY wrote:
> 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
>
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
Dr. Adrian E. Roitberg
Professor.
Quantum Theory Project, Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Mon Nov 03 2014 - 08:00:03 PST
