was this run on a queuing system or interactively? If on a queue, did
not you check that you did not run of time? Did you visualize the MD run
to see if something is wrong?
Maybe rerun the production alone with a smaller value of ntpr and ntwx
and see if it still stops and then look at the mdout and the mdcrd.
adrian
On 10/23/15 10:10 AM, Atila Petrosian wrote:
> I should mention to this note that time of heating, density,
> equilibration phases is 1500 ps, all in all. The time step applied is 0.002
> ps. The time of the first production is 5000 ps.
>
> On Fri, Oct 23, 2015 at 5:10 PM, Atila Petrosian <atila.petrosian.gmail.com>
> wrote:
>
>> Dear amber users
>>
>> I am doing MD simulation of protein-ligand system. Energy minimization,
>> heating, density, equilibration and the first production phases were done
>> without any problem. But the second production phases (2500000 steps) was
>> stopped after 85000 steps. I saw the out file. End of the file is as
>> follows:
>>
>>
>> ------------------------------------------------------------------------------
>>
>> NSTEP = 82500 TIME(PS) = 6665.000 TEMP(K) = 299.55 PRESS =
>> -2.4
>> Etot = -89114.7196 EKtot = 23147.6081 EPtot =
>> -112262.3277
>> BOND = 942.5063 ANGLE = 2609.5307 DIHED =
>> 3466.6091
>> 1-4 NB = 1185.4238 1-4 EEL = 13963.9251 VDWAALS =
>> 12488.6944
>> EELEC = -146919.0171 EHBOND = 0.0000 RESTRAINT =
>> 0.0000
>> EKCMT = 9711.0429 VIRIAL = 9730.5119 VOLUME =
>> 374960.9897
>> Density =
>> 1.0272
>> Ewald error estimate: 0.9482E-04
>>
>> ------------------------------------------------------------------------------
>>
>> NSTEP = 85000 TIME(PS) = 6670.000 TEMP(K) = 299.57 PRESS =
>> 2.4
>> Etot = -89066.4258 EKtot = 23149.4140 EPtot =
>> -112215.8399
>> BOND = 991.3283 ANGLE = 2577.5157 DIHED =
>> 3428.6864
>> 1-4 NB = 1192.5987 1-4 EEL = 13939.8682 VDWAALS =
>> 12363.0791
>> EELEC = -146708.9164 EHBOND = 0.0000 RESTRAINT =
>> 0.0000
>> EKCMT = 9733.2468 VIRIAL = 9714.2110 VOLUME =
>> 374550.4104
>> Density =
>> 1.0284
>> Ewald error estimate: 0.7201E-04
>>
>> ------------------------------------------------------------------------------
>>
>> There was Ewald error estimate in the first production phase. But the
>> first production phase was ended, normally.
>>
>> What is the reason of stopping sander?
>>
>> I used following commands:
>>
>> mpirun -np 8 $AMBERHOME/bin/sander.MPI -O -i min.in -o min.out -p
>> comp_sol.prmtop -c comp_sol.inpcrd -r min.rst -ref comp_sol.inpcrd -inf
>> min_info
>>
>> mpirun -np 8 $AMBERHOME/bin/sander.MPI -O -i heat.in -o heat.out -p
>> comp_sol.prmtop -c min.rst -r heat.rst -x heat.mdcrd -ref min.rst -inf
>> heat_info
>>
>> mpirun -np 8 $AMBERHOME/bin/sander.MPI -O -i density.in -o density.out -p
>> comp_sol.prmtop -c heat.rst -r density.rst -x density.mdcrd -ref heat.rst
>> -inf density_info
>>
>> mpirun -np 8 $AMBERHOME/bin/sander.MPI -O -i equil.in -o equil.out -p
>> comp_sol.prmtop -c density.rst -r equil.rst -x equil.mdcrd -inf equil_info
>>
>> mpirun -np 8 $AMBERHOME/bin/sander.MPI -O -i prod.in -o prod1.out -p
>> comp_sol.prmtop -c equil.rst -r prod1.rst -x prod1.mdcrd -inf prod1_info
>>
>> mpirun -np 8 $AMBERHOME/bin/sander.MPI -O -i prod.in -o prod2.out -p
>> comp_sol.prmtop -c prod1.rst -r prod2.rst -x prod2.mdcrd -inf prod2_info
>>
>> Any help will highly appreciated.
>>
>> Best,
>> Atila
>>
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--
Dr. Adrian E. Roitberg
Professor.
Department of Chemistry
University of Florida
roitberg.ufl.edu
352-392-6972
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Received on Fri Oct 23 2015 - 07:30:07 PDT
