Thank you for the help, Christoph. I tried making the changes suggested (Scale = 10; kBT=1) but I got the following error at step_001:
ERROR: Lost atoms: original 4096 current 0 (src/thermo.cpp:439)
Last command: run 10000
I am attaching my settings.xml and input file (sc.in) for reference.
Since my target RDF is also in reduced units (generated using LAMMPS),
unlike gromacs units which was in spce-ibi_lammps tutorial, I next tried
making changes by keeping the scale=1 (since both target RDF and lammps
have same reduced units) and this time the lammps simulations ran but I got
error while rdf calculations in step_001:
Calculating rdfs with csg_stat using 4 tasks
Running critical command 'csg_stat --nt 4 --options
/home/rajat/Desktop/Inverse_Design/settings.xml --top input.data --trj
traj.dump --begin 0 --first-frame 0'
begin to calculate distribution functions
# of bonded interactions: 0
# of non-bonded interactions: 1
WARNING: The votca lammps data reader is only able to read lammps files
formatted in the following styles:
angle
atom
bond
full
molecule
These styles use the following formats in the atom block:
atom-ID molecule-ID atom-type charge x y z
atom-ID molecule-ID atom-type charge x y z nx ny nz
atom-ID molecule-ID atom-type x y z
atom-ID molecule-ID atom-type x y z nx ny nz
atom-ID atom-type x y z
atom-ID atom-type x y z nx ny nz
.
.
.
I have 4096 beads in 4096 molecules
Reading frame, timestep 10000
an error occurred:
The max of interaction "CG-CG" bigger is than half the box.
Callstack:
/home/rajat/share/votca/scripts/inverse/inverse.sh - linenumber 266
do_external - linenumber 176 in
/home/rajat/share/votca/scripts/inverse/functions_common.sh
/home/rajat/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')
/home/rajat/share/votca/scripts/inverse/calc_rdf_generic.sh - linenumber 84
critical - linenumber 4 (see 'csg_call --cat
function critical')
die - linenumber 2 (see 'csg_call --cat
function die')
I'm trying to perform IBI calculations for a simple cubic lattice. Is there
anything that I'm missing or doing wrong?
Any help is appreciated.
Thanks,
Rajat
On Sunday, May 31, 2020 at 5:43:48 PM UTC+5:30, Christoph Junghans wrote:
>
>
>
> On Sun, May 31, 2020, 05:47 Rajat Gupta <[email protected]
> <javascript:>> wrote:
>
>> Hello everyone,
>>
>> I am new to using VOTCA and have some queries. I am working in coarse
>> graining using VOTCA and used LAMMPS to generate my target RDF (in reduced
>> units).
>>
>> While going through ibi_lammps tutorial in VOTCA, I saw the unit
>> conversion done for LAMMPS real units.
>>
>> Can anyone please suggest me the changes I need to make in my
>> "settings.xml" in order to perform IBI calculations and handle the lj units?
>>
> VOTCA always assumes lammps files are in angstroms even if they are in LJ
> units and then converts them to it's internal units, nm. And writes the rdf
> and potentials out in nm as well.
> That means for a setup in LJ units the potential will be in LJ*(angstroms
> to nm conversion) [0.1].
> Hence you a basically just have to scale the potential back to LJ units by
> scaling everything with a factor 10 using the "scale" parameter in the
> settings file. That covers the x axis, for the y axis you just have to set
> the 'kBT' parameter to the right unitless value for the temperature you are
> calculating. kBT is the only unit parameter used in ibi.
>
> Christoph
>
>>
>> Thanks,
>> Rajat
>>
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sc.in
Description: Binary data
settings.xml
Description: XML document
