Dear Bert,
I am very new to molecular dynamics calculations, but I want to learn.
I think I must have misunderstood the usage of this functionality. Here is my input:
title "peptide preparation"
echo
start pep
prepare
source pep.pdb
new_top new_seq
new_rst
periodic
center
orient
solvate
update lists
ignore
write pep_ref.rst
write pep_ref.pdb
end
task prepare
After the preparation of the restart file
echo
title "NWChem polarized forcefield test"
memory noverify heap 1 mb stack 32 mb global 8 mb
start pep
prepare
read pep_ref.rst
write pep_fslu.rst
end
task prepare
md
system pep_fslu
fix solute
sd 100
end
task md optimize
task shell "cp pep_fslu.qrs pep_fsol.rst"
md
system pep_fsol
fix solvent
sd 100
end
task md optimize
task shell "cp pep_fsol.qrs pep_dyn.rst"
md
system pep_dyn
step 0.001 equil 0 data 10
polar scf 12 0.001
shake 100 0.0001
cutoff 0.9
leapfrog
isotherm 298.15 trelax 0.1
isobar 1.025e5 trelax 0.4 compress 4.53e-10
print step 1 stat 10
update pairs 1 center 0 long 1 rdf 0
record rest 0
record prop 0 sync 1
record coord 0
record veloc 0
test 10
end
task md dynamics
This runs with error, but if I comment out "polar scf 12 0.001" the calculation finished without error. I assume that I can use this method to calculate self-consistent polarization force field for every molecule when running md simulations. What I don't understand is that whether I need to provide the polarization in the segment file or not.
Many thanks for your patience.
The error message is
Parameter files used to resolve force field parameters
/opt/nwchem_intel2013_openmpi16/data/amber_s/amber.par
/opt/nwchem_intel2013_openmpi16/data/amber_q/amber.par
/opt/nwchem_intel2013_openmpi16/data/amber_x/amber.par
/opt/nwchem_intel2013_openmpi16/data/amber_u/amber.par
./amber.par
Using existing topology pep.top
Topology pep.top
Restart generation using command file directives
Read restart pep_ref.rst
Created restart pep_fslu.rst
Task times cpu: 0.0s wall: 0.1s
NWChem Input Module
-------------------
Task times cpu: 0.6s wall: 1.1s
NWChem Input Module
-------------------
Task times cpu: 0.0s wall: 0.0s
NWChem Input Module
-------------------
Task times cpu: 0.1s wall: 0.3s
NWChem Input Module
-------------------
Task times cpu: 0.0s wall: 0.0s
NWChem Input Module
-------------------
0:Segmentation Violation error, status=: 11
(rank:0 hostname:localhost.localdomain pid:4693):ARMCI DASSERT fail. ../../ga-5-1/armci/src/common/signaltrap.c:SigSegvHandler():310 cond:0
Last System Error Message from Task 0:: Inappropriate ioctl for device
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI COMMUNICATOR 4 DUP FROM 0
with errorcode 11.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
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