From NWChem
You are viewing a single post from the thread title above
|
|
|
Clicked A Few Times
Threads 28
Posts 31
|
|
| 10:56:16 PM PDT - Thu, Aug 9th 2012 |
|
I first used gromacs 4.5.3 to run MD simulation (force field: Amber FF99SB). Then I run QM/MM simulation with NWCHEM 6.0. But nwchem could not carry out QM/MM calculation.
The error meesage disppeared as follow. How can I solve this problem?
in qmmm_input:
out of qmmm_input:
****************************************************
* NWChem QM/MM Interface Module *
* *
* Developed Marat Valiev 2004 *
****************************************************
QM/MM Interface Parameters
--------------------------
operation task:operation optimize
reference energy qmmm:uqmatm 0.000000 <--- Warning zero value is not advisable !!!
bqzone radius qmmm:bqzone 10.000000
excluded bq's qmmm:bq_exclude none
link atom type qmmm:linkatm hydrogens
optimization method qmmm:optimization bfgs
qmmm:region 0 qmlink
qmmm:region 0 mm_solute
qmmm:region 0 solvent
ecp on link atoms qmmm:link_ecp auto
interface api qmmm:interface qm
------------------------------------------------------
0:0:nga_put_common:cannot locate region: [28099:38542 ,28099:38542 ]:: -999
(rank:0 hostname:k104.hn.org pid:26977):ARMCI DASSERT fail. armci.c:ARMCI_Error():260 cond:0
Last System Error Message from Task 0:: Inappropriate ioctl for device
[k104.hn.org:26977] MPI_ABORT invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 0
Last System Error Message from Task 7:: No such file or directory
forrtl: error (78): process killed (SIGTERM)
Last System Error Message from Task 1:: No such file or directory
forrtl: error (78): process killed (SIGTERM)start 1Q3W
Last System Error Message from Task 2:: No such file or directory
forrtl: error (78): process killed (SIGTERM)
Last System Error Message from Task 3:: No such file or directory
forrtl: error (78): process killed (SIGTERM)
Last System Error Message from Task 4:: No such file or directory
forrtl: error (78): process killed (SIGTERM)
Last System Error Message from Task 5:: No such file or directory
forrtl: error (78): process killed (SIGTERM)
Last System Error Message from Task 6:: No such file or directory
forrtl: error (78): process killed (SIGTERM)
The prepare.nw is as follow:
permanent_dir ./perm
scratch_dir ./data
prepare
system 1Q3W_opt
source 4.pdb
vacuo
box 8.04594 9.19135 7.56676
new_top new_seq
new_rst
modify atom 85:_CB quantum
modify atom 85:2HB quantum
modify atom 85:3HB quantum
modify atom 85:_CG quantum
modify atom 85:2HG quantum
modify atom 85:3HG quantum
modify atom 85:_CD quantum
modify atom 85:2HD quantum
modify atom 85:3HD quantum
modify atom 85:_CE quantum
modify atom 85:2HE quantum
modify atom 85:3HE quantum
modify atom 85:_NZ quantum
modify atom 85:2HZ quantum
modify atom 85:3HZ quantum
modify atom 85:4HZ quantum
modify segment 384 quantum
update lists
ignore
write 1Q3W_opt.pdb
write 1Q3W_opt.rst
end
task prepare
The QM/MM simulation parameters are:
echo
start 1Q3W
memory total 6000 Mb
permanent_dir ./perm
scratch_dir ./data
prepare
read 1Q3W_opt.rst
write 1Q3W_opt_bak_1.rst
end
task prepare
basis
* library 6-31g*
end
driver
maxiter 400
end
scf
singlet
rhf
maxiter 400
direct
print "parameters"
print "information"
print "convergence"
end
dft
xc b3lyp
iterations 400
print "coulomb fit"
print "intermediate energy info"
print "intermediate evals"
end
md
system 1Q3W_opt
sd 2000 init 0.01 min 1.0e-5 max 0.05
cutoff 1.0 qmmm 1.0
noshake solute
msa 6000
mwm 11000
print step 1 extra
print energies 1
end
qmmm
region qmlink mm_solute solvent
method bfgs sd sd
maxiter 400 2000 2000
ncycles 60
density espfit
end
task qmmm dft optimize
prepare
read 1Q3W_opt.rst
write 1Q3W_opt_final_1.pdb
end
task prepare
|
|
|
AWC's:
2.5.10 MediaWiki - Stand Alone Forum Extension
Forum theme style by: AWC
