Hello,
I spent some days figuring out how to perform quantum hop molecular dynamics simulations but I'm getting some strange errors in when running the prepare module. I have read the NWChem documentation (specially that about the prepare and MD modules) and some articles (AKBARI, Saeed, et al. ChemPhysChem, 2017, vol. 18, no 23, p. 3485-3497, Devanathan, Ram, et al. The Journal of Physical Chemistry B 114.43 (2010): 13681-13690...) that have performed these simulations but I could't find any example or specific working input files.
I'm trying to take the example of benzene [1] from the NWChem repository and modify it to run a single benzene molecule solvated in water allowing proton hopping. Here is the content of my "benzene.nw" file based on that of the example and modifying it according to the documentation:
start benzene
prepare
system benzene_em
new_top new_seq
solvate
modify segment 1 protonation 1
update lists
ignore
qhop
end
task prepare
When run this input file I get the following output:
argument 1 = benzene.nw
Northwest Computational Chemistry Package (NWChem) 6.6
------------------------------------------------------
Environmental Molecular Sciences Laboratory
Pacific Northwest National Laboratory
Richland, WA 99352
Copyright (c) 1994-2015
Pacific Northwest National Laboratory
Battelle Memorial Institute
NWChem is an open-source computational chemistry package
distributed under the terms of the
Educational Community License (ECL) 2.0
A copy of the license is included with this distribution
in the LICENSE.TXT file
ACKNOWLEDGMENT
--------------
This software and its documentation were developed at the
EMSL at Pacific Northwest National Laboratory, a multiprogram
national laboratory, operated for the U.S. Department of Energy
by Battelle under Contract Number DE-AC05-76RL01830. Support
for this work was provided by the Department of Energy Office
of Biological and Environmental Research, Office of Basic
Energy Sciences, and the Office of Advanced Scientific Computing.
Job information
---------------
hostname = sun014
program = /opt/nwchem-6.6/bin/LINUX64/nwchem
date = Mon Mar 11 12:37:50 2019
compiled = Thu_Mar_07_12:05:29_2019
source = /opt/nwchem-6.6
nwchem branch = 6.6
nwchem revision = 27746
ga revision = 10594
input = benzene.nw
prefix = benzene.
data base = ./benzene.db
status = startup
nproc = 1
time left = -1s
Memory information
------------------
heap = 13107196 doubles = 100.0 Mbytes
stack = 13107201 doubles = 100.0 Mbytes
global = 26214400 doubles = 200.0 Mbytes (distinct from heap & stack)
total = 52428797 doubles = 400.0 Mbytes
verify = yes
hardfail = no
Directory information
---------------------
0 permanent = .
0 scratch = .
NWChem Input Module
-------------------
Prepare Module
--------------
Force field amber
Directories used for fragment and segment files
/opt/nwchem-6.6/src/data/amber_s/
/opt/nwchem-6.6/src/data/amber_q/
/opt/nwchem-6.6/src/data/amber_x/
/opt/nwchem-6.6/src/data/amber_u/
./
Parameter files used to resolve force field parameters
/opt/nwchem-6.6/src/data/amber_s/amber.par
/opt/nwchem-6.6/src/data/amber_q/amber.par
/opt/nwchem-6.6/src/data/amber_x/amber.par
/opt/nwchem-6.6/src/data/amber_u/amber.par
./amber.par
Deleted existing topology benzene.top
Deleted existing sequence ./benzene.seq
PDB geometry benzene.pdb
Created sequence ./benzene.seq
Parameter file /opt/nwchem-6.6/src/data/amber_s/amber.par
Parameter file /opt/nwchem-6.6/src/data/amber_q/amber.par
Parameter file /opt/nwchem-6.6/src/data/amber_x/amber.par
Parameter file /opt/nwchem-6.6/src/data/amber_u/amber.par
Total charge 0.000000
qhop_setup
Program received signal SIGSEGV: Segmentation fault - invalid memory reference.
Backtrace for this error:
#0 0x7f1e51eab89d in ???
#1 0x7f1e51eaaae3 in ???
#2 0x7f1e51752fbf in ???
#3 0x56345fcbf5e2 in ???
#4 0x56345fcc341a in ???
#5 0x56345f5b3530 in ???
#6 0x56345f571d72 in ???
#7 0x56345f54c42f in ???
#8 0x56345ec5cf11 in task_
at /opt/nwchem-6.6/src/task/task.F:340
#9 0x56345ec54f18 in nwchem
at /opt/nwchem-6.6/src/nwchem.F:285
#10 0x56345ec5555f in main
at /opt/nwchem-6.6/src/nwchem.F:369
-------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
-------------------------------------------------------
If I remove the qhop in the input file there is no error in the output so my guess is that I am missing some kind of input information or something else. I am pretty sure that my NWChem installation is correct (I can run all the examples: dft, md, optimization...).
I was wondering to know if someone could provide a simple working example, e.g. q-hop in pure water or maybe with a simple molecule solvated, or let me know if there is some trick that I'm missing.
Thank you very much in advance.
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