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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Received on Fri Oct 23 2015 - 07:30:05 PDT
