Hi everyone,
I tried making ntpr=1. I got some results in my out file I am
attaching part of it below.
Also i got an GPU error:
*cudaMemcpy GpuBuffer::Download failed an illegal memory access was
encountered*
The simulation has already run for 567 ns now but i am unable to
extend it further. (I mistakenly wrote 200 ns earlier. I confused it with
another currently progressing simulation of the same protein)
Additionally the topology was prepared using non-bonded restraints
involving ATP, water, Mg ions using MCPB.py
ATP is bound to water and Mg ion but not bound to protein in any way.
I am using AMBER 14 for this work.
How can i diagnose and correct the issue.
=============================================================
NSTEP = 1 TIME(PS) = 567820.002 TEMP(K) = 320.28 PRESS =
-9.7
Etot = 1515575.3180 EKtot = 133929.7344 EPtot =
1381645.5836
BOND = 4274.5699 ANGLE = 11446.5975 DIHED =
17453.5927
1-4 NB = 5080.8066 1-4 EEL = 62404.6045 VDWAALS =
78331.1990
EELEC = -799224.4358 EHBOND = 0.0000 RESTRAINT =
2001878.6492
EAMBER (non-restraint) = -620233.0656
EKCMT = 54808.4105 VIRIAL = 55242.9365 VOLUME =
2077945.3372
Density =
1.0035
------------------------------------------------------------------------------
NMR restraints: Bond =********* Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 2 TIME(PS) = 567820.004 TEMP(K) =********* PRESS =
86553.6
Etot = ************** EKtot = ************** EPtot =
1919806.7977
BOND = 4529.0777 ANGLE = 11556.5341 DIHED =
17459.8895
1-4 NB = 5088.5583 1-4 EEL = 62410.2871 VDWAALS =
683134.7914
EELEC = -799273.4419 EHBOND = 0.0000 RESTRAINT =
1934901.1014
EAMBER (non-restraint) = -15094.3037
EKCMT = 76292.8114 VIRIAL = -3806972.9795 VOLUME =
2077944.3469
Density =
1.0035
------------------------------------------------------------------------------
NMR restraints: Bond =********* Angle = 0.000 Torsion = 0.000
===============================================================================
NSTEP = 3 TIME(PS) = 567820.006 TEMP(K) = NaN PRESS
=********
Etot = NaN EKtot = NaN EPtot =
45293561.3628
BOND = 7487.4039 ANGLE = 12035.7977 DIHED =
17463.2835
1-4 NB = 374769.4957 1-4 EEL = 62425.8482 VDWAALS =
1508870.1977
EELEC = -795873.2254 EHBOND = 0.0000 RESTRAINT =
44106382.5615
EAMBER (non-restraint) = 1187178.8013
EKCMT = -12527120.5171 VIRIAL = -4050121.5964 VOLUME =
2085965.7275
Density =
0.9996
------------------------------------------------------------------------------
=============================================================
On Sat, Feb 24, 2018 at 7:22 PM, Abhilash J <md.scfbio.gmail.com> wrote:
>
>
> Thanks for the help i will try this and check if the results point to some
> issue.
> I will get back as soon as i get some relevent information.
>
> On Fri, Feb 23, 2018 at 11:59 PM, David A Case <david.case.rutgers.edu>
> wrote:
>
>> On Fri, Feb 23, 2018, Abhilash J wrote:
>> >
>> > I have a protein-2ATP complex. I ran the simulation using AMBER 14 for
>> > near about 200 ns in steps of 10 ns each. Now all of a sudden it does
>> not
>> > start using the last rst file of last step. I had a look at the rst
>> file it
>> > is complete and nothing else seems suspicious in it. I am able to make a
>> > valid pdb file ( without any stretching/banding of structure) using it.
>> The
>> > out file also does not have any error. It simply writes the inputs used
>> > followed by results section. The section is empty of any results or
>> error.
>> > How can i diagnose this issue. For now i have started the simulation
>> back
>> > from 180 ns to see if it stalls again at 200 ns. But i have kept the old
>> > rst and out files for debugging.
>>
>> Did you try a restart run with ntpr=1 (and a short nstlim)? This might
>> give
>> you more information about what is going wrong. Ordinarily, on a restart,
>> Amber will not print anything until the first ntpr printout. So, setting
>> ntpr=1 has the potential for helping provide more info.
>>
>> .....dac
>>
>>
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Tue Mar 06 2018 - 06:00:04 PST
