Dear amber users,
I did simulations using a simple script like this:
#!/bin/bash
mpiexec -np 24 sander.MPI -O -i min1.in -o min1.out -p com_solv.prmtop -c
com_solv.inpcrd -r min1.rst -ref com_solv.inpcrd
mpiexec -np 24 sander.MPI -O -i min2.in -o min2.out -p com_solv.prmtop -c
min1.rst -r min2.rst -ref min1.rst
mpiexec -np 24 sander.MPI -O -i min3.in -o min3.out -p com_solv.prmtop -c
min2.rst -r min3.rst -ref min2.rst
mpiexec -np 24 sander.MPI -O -i heat.in -o heat.out -p com_solv.prmtop -c
min3.rst -r heat.rst -x heat.mdcrd -ref min3.rst
mpiexec -np 24 sander.MPI -O -i density.in -o density.out -p
com_solv.prmtop -c heat.rst -r density.rst -x density.mdcrd -ref heat.rst
mpiexec -np 24 sander.MPI -O -i equil.in -o equil.out -p com_solv.prmtop -c
density.rst -r equil.rst -x equil.mdcrd -ref density.rst
mpiexec -np 24 pmemd.MPI -O -i md.in -o md1.out -p com_solv.prmtop -c
equil.rst -r md1.rst -x md1.mdcrd -ref equil.rst
mpiexec -np 24 pmemd.MPI -O -i md.in -o md2.out -p com_solv.prmtop -c
md1.rst -r md2.rst -x md2.mdcrd -ref md1.rst
mpiexec -np 24 pmemd.MPI -O -i md.in -o md3.out -p com_solv.prmtop -c
md2.rst -r md3.rst -x md3.mdcrd -ref md2.rst
mpiexec -np 24 pmemd.MPI -O -i md.in -o md4.out -p com_solv.prmtop -c
md3.rst -r md4.rst -x md4.mdcrd -ref md3.rst
mpiexec -np 24 pmemd.MPI -O -i md.in -o md5.out -p com_solv.prmtop -c
md4.rst -r md5.rst -x md5.mdcrd -ref md4.rst
I found that simulation of md3 was initiated even when md2 was not
finished. Why did this situation happen? I just can't understand, I believe
that it should be done one by one.
Here is the tail of md2.out:
NSTEP = 145000 TIME(PS) = 2990.000 TEMP(K) = 299.49 PRESS =
248.5
Etot = -88189.9096 EKtot = 23286.5936 EPtot =
-111476.5032
BOND = 1205.5344 ANGLE = 3119.5057 DIHED =
4059.5307
1-4 NB = 1454.1815 1-4 EEL = 16306.6244 VDWAALS =
11500.7194
EELEC = -149122.5994 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 9485.1442 VIRIAL = 7488.8395 VOLUME =
372081.3656
Density =
1.0401
Ewald error estimate: 0.5480E-04
------------------------------------------------------------------------------
And here is the head lines of md3.out:
NSTEP = 5000 TIME(PS) = 3000.400 TEMP(K) = 299.67 PRESS =
285.1
Etot = -88153.7618 EKtot = 23300.6323 EPtot =
-111454.3941
BOND = 1195.8181 ANGLE = 3150.6217 DIHED =
4032.4322
1-4 NB = 1423.9929 1-4 EEL = 16243.0419 VDWAALS =
11112.8508
EELEC = -148613.1517 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 9392.6117 VIRIAL = 7096.5505 VOLUME =
372965.9791
Density =
1.0377
Ewald error estimate: 0.8542E-04
------------------------------------------------------------------------------
NSTEP = 10000 TIME(PS) = 3010.400 TEMP(K) = 298.89 PRESS =
63.4
Etot = -88427.8110 EKtot = 23240.5069 EPtot =
-111668.3178
BOND = 1124.4801 ANGLE = 3105.8506 DIHED =
4023.7330
1-4 NB = 1452.2233 1-4 EEL = 16273.2497 VDWAALS =
11381.0661
EELEC = -149028.9206 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 9328.4415 VIRIAL = 8818.4310 VOLUME =
372613.5200
Density =
1.0387
Ewald error estimate: 0.4204E-04
------------------------------------------------------------------------------
It seems a little strange that the time begins with 3000.400. For this
problem, is it OK for the trajectory? Thanks very much!
--
Best Regards,
Qinghua
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Received on Wed Dec 14 2011 - 14:00:02 PST
