Hi Adrian,
Thanks for the quick reply. In my case only one job is running.
Thanks, Ibrahim
On Mon, Nov 3, 2014 10:55 AM, Adrian Roitberg <roitberg.ufl.edu> wrote:
>
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
>
>
>_______________________________________________
>AMBER mailing list
>AMBER.ambermd.org
>http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
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 - 08:00:04 PST
