Dear all, I am learning to use VOTCA with LAMMPS and the IBI method, and have successfully tested the spce example and coarse-grained a monoatomic material.
Now, I am trying to make a dodecane chain model of structure A-B-B-A, and
using the hexane example as a reference to create the setting, mapping and
topology files. The LAMMPS files for the coarse-grained dodecane have been
tested and work fine. Actually, I am getting errors just after the LAMMPS
run of the first iteration. These errors are related to the topology file
topol.top. In first place, the error was related to the absence of this
file (not needed in the monoatomic case), and now that I am using an
adaptation of the hexane's topol.top file, it is the format to blame
according to inverse.log:
Calculating rdfs with csg_stat using 8 tasks
Running critical command 'csg_stat --nt 8 --options
/home/jjbm/Documents/Molecules/Topologies/SimpleExamples/Dodecane/CG_Dodecane/cg_450K/test_nononbonded/settings.xml
--top topol.top --trj traj.dump --begin 0 --$
begin to calculate distribution functions
# of bonded interactions: 0
# of non-bonded interactions: 3
an error occurred:
input format not supported: topol.top
Callstack:
~/share/votca/scripts/inverse/inverse.sh - linenumber 264
do_external - linenumber 176 in ~
/share/votca/scripts/inverse/functions_common.sh
~/share/votca/scripts/inverse/update_ibi.sh - linenumber 31
for_all - linenumber 22 (see 'csg_call --cat function for_all')
do_external - linenumber 19 (see 'csg_call --cat
function do_external')
~/share/votca/scripts/inverse/calc_rdf_generic.sh -
linenumber 79
critical - linenumber 4 (see 'csg_call --cat
function critical')
die - linenumber 2 (see 'csg_call --cat
function die')
####################################################################################################################################################################################################################$
#
$
#
ERROR:
$
# critical: 'csg_stat --nt 8 --options /test_nononbonded/settings.xml --top
topol.top --trj traj.dump --begin 0 --first-frame 0$
# For details see the logfile
/test_nononbonded/inverse.log
$
#
$
####################################################################################################################################################################################################################$
die: (called from 9953) CSG_MASTER_PID is 6366
die: pids to kill: 0
Attached are the three files corresponding to this molecule. Since I have
never used GROMACS, I am not sure what I am doing wrong there. Any help?
Thanks in advance,
Kind regards
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topol.top
Description: Binary data
settings.xml
Description: XML document
dodecane_cg.xml
Description: XML document
