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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Received on Fri Oct 23 2015 - 07:00:04 PDT
