On Wed, Jul 14, 2021 at 6:30 PM Rishabh Guha <[email protected]> wrote: > > By update rate I mean the variable which is set as 'weight' in settings.xml > file. > <post_add_options> > <!-- convergence check options --> > <convergence> > <!-- for RE we check change in potentials/parameters (new-cur) --> > <what>pot</what> > <weight>1.0</weight> > <base>cur</base> > <norm>2</norm> > </convergence> > <average> > <what>param pot</what> > </average> > </post_add_options> > > Another thing which we wanted to discuss with you is this :- > The initial range of r (min and cutoff) are in nm in the settings file. So > when we are calculating the lj potential:- > > C12/r^12 - C6/r^6, the r is in nm. > > In this case, C12 and C6 should also be in the respective units. So if our > initial assumption is suppose sigma = 5A(0.5 nm) and epsilon = 0.1 kj/mol, > the initial param.init values should be:- > > 0 0.0000975625 i > 1 0.00625 i > > If these are the initial units, we start getting negative values for > CG-CG.pot from the second iteration and get an error. Are we setting these > initial values correctly? Sorry, the C6, C12 parameter need to be in nm and kj/mol, too 0.1/0.5**6 and 0.1/0.5**12 (maybe I forgot a factor 4 here) and you have to convert them before putting them in the lammps script.
Christoph > > On Wed, Jul 14, 2021 at 8:22 PM Christoph Junghans <[email protected]> wrote: >> >> >> >> On Wed, Jul 14, 2021 at 14:35 Rishabh Guha <[email protected]> wrote: >>> >>> Thanks! Is there anything which can basically increase the update rate / >>> gradient per iteration? >> >> What is the update rate? >> >> Christoph >> >>> >>> On Wed, Jul 14, 2021 at 4:15 PM Christoph Junghans <[email protected]> >>> wrote: >>>> >>>> On Wed, Jul 14, 2021 at 2:10 PM Rishabh Guha <[email protected]> wrote: >>>> > >>>> > Hey Christoph, >>>> > >>>> > Thanks for these pointers! They were helpful. We used a slightly >>>> > different approach but we got the parameters to get updated. Can you >>>> > clarify something for us? >>>> > >>>> > We had previously discussed the parameters for the init file in case of >>>> > lj126:- >>>> > The LJ126 inputs are not super-well documented and there is no >>>> > tutorial, but if I remember correctly, the param.init file needs to >>>> > look something like this: >>>> > 1.0 <C6_value> i >>>> > 2 <C12_value> i >>>> > >>>> > Can you confirm whether C6 and C12 are supposed to be what we assume it >>>> > to be? i.e - C12 = 4*epsilon*sigma^12 and C6 = 4*epsilon*sigma^6? Or is >>>> > c12 and C6 just sigma and epsilon here? I tried setting the values as >>>> > C12 = 4*epsilon*sigma^12 and C6 = 4*epsilon*sigma^6. Firstly they are >>>> > huge and secondly they barely change in subsequent iterations >>>> Yes, it is all coefficients combined, see: >>>> https://github.com/votca/csg/blob/master/src/libcsg/potentialfunctions/potentialfunctionlj126.cc#L29 >>>> lam_(0) and lam_(1) are the first and second parameters read from the file! >>>> >>>> Christoph >>>> > >>>> > >>>> > >>>> > On Tue, Jul 13, 2021 at 6:54 PM Christoph Junghans <[email protected]> >>>> > wrote: >>>> >> >>>> >> .sh >>>> >> >>>> >> >>>> >> On Tue, Jul 13, 2021 at 4:31 PM Rishabh Guha <[email protected]> wrote: >>>> >> > >>>> >> > Hey Christoph, >>>> >> > >>>> >> > Sorry for another email. We are trying to get RE with LJ to work but >>>> >> > the potentials are not converging. One question which we have is that >>>> >> > we have to change the pair style from table linear to lj/cut. >>>> >> > >>>> >> > In this case, the pair coefficients won't be extracted from a table. >>>> >> > Do you know of a way which can get us to change the values of epsilon >>>> >> > , sigma and cutoffs in subsequent interations? >>>> >> >>>> >> Yes, the values should be in the param.cur file in each step directory. >>>> >> You will have to customize the script to run the simulation though to >>>> >> copy them out of the parameter file into the lammps input script. >>>> >> >>>> >> To do this do the following: >>>> >> 1.) set <scriptpath> in your xml settings file (see propane/imc >>>> >> tutorial), you can use $PWD, which means the same directory as >>>> >> settings xml is in. >>>> >> 2.) create a file called csg_table in said <scriptpath> directory >>>> >> 3.) add a line to csg_table: >>>> >> run lammps my_run_genericsim.sh >>>> >> 4.) copy run_genericsim.sh from votca/csg/share/script/inverse into >>>> >> the <scriptpath> directory and rename it to my_run_genericsim >>>> >> 5.) modify my_run_genericsim.sh >>>> >> >>>> >> For 5.) you want to add something like >>>> >> sigma=$(awk '(NR==1){print $2}' param.cur) >>>> >> eps=$(awk '(NR==2){print $2}' param.cur) >>>> >> sed -e "s/@SIGMA@/${sigma}/" -e "s/@EPS@/${eps}/' -i lammps.script >>>> >> somewhere before lammps is called. >>>> >> This will extract sigma and eps from param.cur and then replace >>>> >> @SIGMA@ and @EPS@ with the actual values in the simulation script. >>>> >> >>>> >> Maybe lammps can read the coefficients from a file, too, but I am not >>>> >> sure here. >>>> >> >>>> >> Christoph >>>> >> >>>> >> > >>>> >> > >>>> >> > On Tue, Jul 13, 2021, 4:35 PM Christoph Junghans <[email protected]> >>>> >> > wrote: >>>> >> >> >>>> >> >> On Tue, Jul 13, 2021 at 2:27 PM Rishabh Guha <[email protected]> wrote: >>>> >> >> > >>>> >> >> > Hey Christoph, >>>> >> >> > >>>> >> >> > I am currently working on it. I am struggling for it to match up >>>> >> >> > with a target rdf I want it to match up to. A quick question:- >>>> >> >> > <re> >>>> >> >> > <!-- function form for the potential (lj126 or ljg or >>>> >> >> > cbspl)--> >>>> >> >> > <function>lj126</function> >>>> >> >> > <lj126> >>>> >> >> > <!-- no. of knots for cbspl function --> >>>> >> >> > <!-- nknots -->48<!-- /nknots --> >>>> >> >> > </lj126> >>>> >> >> > </re> >>>> >> >> > <inverse> >>>> >> >> > >>>> >> >> > In the cubic spline case we had to mention the number of knots in >>>> >> >> > the settings file. Do we have to mention anything in the lj126 >>>> >> >> > case? Or does the section just become:- >>>> >> >> > >>>> >> >> > <re> >>>> >> >> > <!-- function form for the potential (lj126 or ljg or >>>> >> >> > cbspl)--> >>>> >> >> > <function>lj126</function> >>>> >> >> > <lj126> >>>> >> >> > </lj126> >>>> >> >> > </re> >>>> >> >> Looking at >>>> >> >> https://github.com/votca/csg/blob/master/src/tools/csg_reupdate.cc#L664_L670, >>>> >> >> I don't think lj126 takes any options, so you can delete the whole >>>> >> >> block. >>>> >> >> >>>> >> >> Christoph >>>> >> >> > >>>> >> >> > Thanks >>>> >> >> > >>>> >> >> > On Tue, Jul 13, 2021 at 4:22 PM Christoph Junghans >>>> >> >> > <[email protected]> wrote: >>>> >> >> >> >>>> >> >> >> On Tue, Jul 13, 2021 at 2:07 PM Rishabh Guha <[email protected]> >>>> >> >> >> wrote: >>>> >> >> >> > >>>> >> >> >> > Hey Christoph, >>>> >> >> >> > >>>> >> >> >> > Thanks for the update. Just FYI for future users, the x values >>>> >> >> >> > do matter and the correct format is >>>> >> >> >> > 0 <C6_value> i >>>> >> >> >> > 1 <C12_value> i >>>> >> >> >> Thanks! I believe these are best guesses. >>>> >> >> >> >>>> >> >> >> If you get it working, please contribute an example to >>>> >> >> >> csg-tutorials >>>> >> >> >> and/or write a bit of documentation (see csg/share/doc folder) >>>> >> >> >> for the >>>> >> >> >> website. >>>> >> >> >> >>>> >> >> >> Thanks, >>>> >> >> >> >>>> >> >> >> Christoph >>>> >> >> >> >>>> >> >> >> > >>>> >> >> >> > Can you or Sikander tell me what is the value of C6 or C12 >>>> >> >> >> > here? Is it something like a best guess? >>>> >> >> >> > >>>> >> >> >> > On Tue, Jul 13, 2021 at 11:40 AM Christoph Junghans >>>> >> >> >> > <[email protected]> wrote: >>>> >> >> >> >> >>>> >> >> >> >> On Tue, Jul 13, 2021 at 9:13 AM Rishabh Guha <[email protected]> >>>> >> >> >> >> wrote: >>>> >> >> >> >> > >>>> >> >> >> >> > Hey Christoph, >>>> >> >> >> >> > >>>> >> >> >> >> > Thanks for the help with the lammps executable. VOTCA runs >>>> >> >> >> >> > smoothly now for IBI. We were also looking into RE as we >>>> >> >> >> >> > wanted an LJ analytical form for our CG potential. I am >>>> >> >> >> >> > trying to modify the settings.xml script for re_lammps. For >>>> >> >> >> >> > lj126, I changed the script as:- >>>> >> >> >> >> > >>>> >> >> >> >> > <re> >>>> >> >> >> >> > <!-- function form for the potential (lj126 or ljg or >>>> >> >> >> >> > cbspl)--> >>>> >> >> >> >> > <function>lj126</function> >>>> >> >> >> >> > <lj126> >>>> >> >> >> >> > <!-- no. of knots for cbspl function --> >>>> >> >> >> >> > <!-- nknots -->48<!-- /nknots --> >>>> >> >> >> >> > </lj126> >>>> >> >> >> >> > </re> >>>> >> >> >> >> > >>>> >> >> >> >> > How should I format my CG-CG.param.init file now for lj126. >>>> >> >> >> >> > I deleted the knot values and I just put in 2 best guess >>>> >> >> >> >> > numbers for C12 and C6 in that file(PFA). But that is >>>> >> >> >> >> > throwing up a format error:- >>>> >> >> >> >> > Generating potential tables from the initial parameters >>>> >> >> >> >> > Running critical command 'csg_reupdate --gentable true >>>> >> >> >> >> > --param-in-ext param.new --options >>>> >> >> >> >> > /gpfs/alpine/mat226/proj-shared/Rishabh_copy/votca/csg-tutorials/spce/re_lammps_lys_met/settings.xml' >>>> >> >> >> >> > an error occurred: >>>> >> >> >> >> > invaid type: file CG-CG.param.new, line 1 >>>> >> >> >> >> > >>>> >> >> >> >> > Callstack: >>>> >> >> >> >> > /sw/andes/spack-envs/base/opt/linux-rhel8-x86_64/gcc-9.3.0/votca-csg-2021.1-gkkujagr5jpheolnzjb4t3t2e43lxwbu/share/votca/scripts/inverse/inverse.sh >>>> >> >> >> >> > - linenumber 156 >>>> >> >> >> >> > do_external - linenumber 177 in >>>> >> >> >> >> > /sw/andes/spack-envs/base/opt/linux-rhel8-x86_64/gcc-9.3.0/votca-csg-2021.1-gkkujagr5jpheolnzjb4t3t2e43lxwbu/share/votca/scripts/inverse/functions_common.sh >>>> >> >> >> >> > >>>> >> >> >> >> > /sw/andes/spack-envs/base/opt/linux-rhel8-x86_64/gcc-9.3.0/votca-csg-2021.1-gkkujagr5jpheolnzjb4t3t2e43lxwbu/share/votca/scripts/inverse/prepare_re.sh >>>> >> >> >> >> > - linenumber 39 >>>> >> >> >> >> > critical - linenumber 4 (see 'csg_call --cat >>>> >> >> >> >> > function critical') >>>> >> >> >> >> > die - linenumber 2 (see 'csg_call --cat >>>> >> >> >> >> > function die') >>>> >> >> >> >> > ########################################################################################################################################################################################### >>>> >> >> >> >> > # >>>> >> >> >> >> > >>>> >> >> >> >> > >>>> >> >> >> >> > # >>>> >> >> >> >> > # ERROR: >>>> >> >> >> >> > >>>> >> >> >> >> > >>>> >> >> >> >> > # >>>> >> >> >> >> > # critical: 'csg_reupdate --gentable true --param-in-ext >>>> >> >> >> >> > param.new --options >>>> >> >> >> >> > /gpfs/alpine/mat226/proj-shared/Rishabh_copy/votca/csg-tutorials/spce/re_lammps_lys_met/settings.xml' >>>> >> >> >> >> > failed # >>>> >> >> >> >> > # For details see the logfile >>>> >> >> >> >> > /gpfs/alpine/mat226/proj-shared/Rishabh_copy/votca/csg-tutorials/spce/re_lammps_lys_met/inverse.log >>>> >> >> >> >> > # >>>> >> >> >> >> > # >>>> >> >> >> >> > >>>> >> >> >> >> > >>>> >> >> >> >> > # >>>> >> >> >> >> > ########################################################################################################################################################################################### >>>> >> >> >> >> > >>>> >> >> >> >> > How should I format the param.init file? >>>> >> >> >> >> >>>> >> >> >> >> The LJ126 inputs are not super-well documented and there is no >>>> >> >> >> >> tutorial, but if I remember correctly, the param.init file >>>> >> >> >> >> needs to >>>> >> >> >> >> look something like this: >>>> >> >> >> >> 1.0 <C6_value> i >>>> >> >> >> >> 2 <C12_value> i >>>> >> >> >> >> >>>> >> >> >> >> I believe, the x values don't really matter, however I am not >>>> >> >> >> >> the >>>> >> >> >> >> expert for this method, so maybe Sikandar can comment on this, >>>> >> >> >> >> too! >>>> >> >> >> >> >>>> >> >> >> >> Christoph >>>> >> >> >> >> >>>> >> >> >> >> > Thanks >>>> >> >> >> >> > >>>> >> >> >> >> > On Fri, Jul 9, 2021 at 9:05 AM Christoph Junghans >>>> >> >> >> >> > <[email protected]> wrote: >>>> >> >> >> >> >> >>>> >> >> >> >> >> On Thu, Jul 8, 2021 at 8:50 PM Rishabh Guha >>>> >> >> >> >> >> <[email protected]> wrote: >>>> >> >> >> >> >> > >>>> >> >> >> >> >> > Hey Christoph, >>>> >> >> >> >> >> > >>>> >> >> >> >> >> > I appreciate all the help but there is still a small >>>> >> >> >> >> >> > roadblock I am facing. >>>> >> >> >> >> >> > >>>> >> >> >> >> >> > The xml file as you know has this setting by default :- >>>> >> >> >> >> >> > <!-- general options for inverse script --> >>>> >> >> >> >> >> > <inverse> >>>> >> >> >> >> >> > <!-- votca units 300*0.00831451 kJ/mol --> >>>> >> >> >> >> >> > <kBT>2.49435</kBT> >>>> >> >> >> >> >> > <!-- use lammps as simulation program --> >>>> >> >> >> >> >> > <program> lammps </program> >>>> >> >> >> >> >> > <!-- lammps specific options --> >>>> >> >> >> >> >> > <lammps> >>>> >> >> >> >> >> > <!-- lammps script to run !--> >>>> >> >> >> >> >> > <script>spce.in</script> >>>> >> >> >> >> >> > <!-- topology to be used by csg_stat !--> >>>> >> >> >> >> >> > <topol>spce.data</topol> >>>> >> >> >> >> >> > <!-- traj file created by lammps !--> >>>> >> >> >> >> >> > <traj>traj.dump</traj> >>>> >> >> >> >> >> Sorry, I was a bit unclear, just add >>>> >> >> >> >> >> <command> >>>> >> >> >> >> >> /gpfs/alpine/mat222/proj-shared/rdguha/lammps/build/lmp >>>> >> >> >> >> >> </command> >>>> >> >> >> >> >> right here. >>>> >> >> >> >> >> >>>> >> >> >> >> >> Alternatively, you could also add >>>> >> >> >> >> >> /gpfs/alpine/mat222/proj-shared/rdguha/lammps/build to your >>>> >> >> >> >> >> PATH. >>>> >> >> >> >> >> > </lammps> >>>> >> >> >> >> >> > <initial_configuration>maindir</initial_configuration> >>>> >> >> >> >> >> > <!-- these files are copied for each new run --> >>>> >> >> >> >> >> > <filelist>spce.data spce.in</filelist> >>>> >> >> >> >> >> > <!-- do so many iterations --> >>>> >> >> >> >> >> > <iterations_max>300</iterations_max> >>>> >> >> >> >> >> > <!-- ibi: inverse biltzmann imc: inverse monte carlo >>>> >> >> >> >> >> > --> >>>> >> >> >> >> >> > <method>ibi</method> >>>> >> >> >> >> >> > </inverse> >>>> >> >> >> >> >> > >>>> >> >> >> >> >> > I changed it to :- >>>> >> >> >> >> >> > <!-- general options for inverse script --> >>>> >> >> >> >> >> > <inverse> >>>> >> >> >> >> >> > <!-- votca units 300*0.00831451 kJ/mol --> >>>> >> >> >> >> >> > <kBT>2.49435</kBT> >>>> >> >> >> >> >> > <!-- use lammps as simulation program --> >>>> >> >> >> >> >> > <program> >>>> >> >> >> >> >> > /gpfs/alpine/mat222/proj-shared/rdguha/lammps/build/lmp >>>> >> >> >> >> >> > (path to my lammps executable) <program> >>>> >> >> >> >> >> > <!-- lammps specific options --> >>>> >> >> >> >> >> > <lammps> >>>> >> >> >> >> >> > <!-- lammps script to run !--> >>>> >> >> >> >> >> > <script>spce.in</script> >>>> >> >> >> >> >> > <!-- topology to be used by csg_stat !--> >>>> >> >> >> >> >> > <topol>spce.data</topol> >>>> >> >> >> >> >> > <!-- traj file created by lammps !--> >>>> >> >> >> >> >> > <traj>traj.dump</traj> >>>> >> >> >> >> >> > </lammps> >>>> >> >> >> >> >> > <initial_configuration>maindir</initial_configuration> >>>> >> >> >> >> >> > <!-- these files are copied for each new run --> >>>> >> >> >> >> >> > <filelist>spce.data spce.in</filelist> >>>> >> >> >> >> >> > <!-- do so many iterations --> >>>> >> >> >> >> >> > <iterations_max>300</iterations_max> >>>> >> >> >> >> >> > <!-- ibi: inverse biltzmann imc: inverse monte carlo >>>> >> >> >> >> >> > --> >>>> >> >> >> >> >> > <method>ibi</method> >>>> >> >> >> >> >> > </inverse> >>>> >> >> >> >> >> > >>>> >> >> >> >> >> > But now, I get this error :- >>>> >> >> >> >> >> > >>>> >> >> >> >> >> > For a more verbose log see: inverse.log >>>> >> >> >> >> >> > We are doing Method: ibi >>>> >> >> >> >> >> > ############################################################################################################################ >>>> >> >> >> >> >> > # >>>> >> >> >> >> >> > >>>> >> >> >> >> >> > # >>>> >> >> >> >> >> > # ERROR: >>>> >> >> >> >> >> > >>>> >> >> >> >> >> > # >>>> >> >> >> >> >> > # source_wrapper: Could not get any script from tags >>>> >> >> >> >> >> > 'functions' >>>> >> >> >> >> >> > '/gpfs/alpine/mat222/proj-shared/rdguha/lammps/build/lmp' >>>> >> >> >> >> >> > # >>>> >> >> >> >> >> > # For details see the logfile >>>> >> >> >> >> >> > /gpfs/alpine/mat226/proj-shared/Rishabh_copy/votca/csg-tutorials/spce/ibi_lammps/inverse.log >>>> >> >> >> >> >> > # >>>> >> >> >> >> >> > # >>>> >> >> >> >> >> > >>>> >> >> >> >> >> > # >>>> >> >> >> >> >> > ############################################################################################################################ >>>> >> >> >> >> >> > >>>> >> >> >> >> >> > Alternatively you can set the cg.inverse.lammps.command >>>> >> >> >> >> >> > in your xml file. >>>> >> >> >> >> >> > I hope setting the path to my lammps executable is what >>>> >> >> >> >> >> > is meant by this >>>> >> >> >> >> >> > >>>> >> >> >> >> >> > >>>> >> >> >> >> >> > On Thu, Jul 8, 2021 at 4:14 PM Christoph Junghans >>>> >> >> >> >> >> > <[email protected]> wrote: >>>> >> >> >> >> >> >> >>>> >> >> >> >> >> >> On Thu, Jul 8, 2021 at 11:04 AM Rishabh Guha >>>> >> >> >> >> >> >> <[email protected]> wrote: >>>> >> >> >> >> >> >> > >>>> >> >> >> >> >> >> > Hey Christoph, >>>> >> >> >> >> >> >> > >>>> >> >> >> >> >> >> > Thanks for the input. I was going over the tutorials >>>> >> >> >> >> >> >> > and I think in my case, the ibi_lammps should work if >>>> >> >> >> >> >> >> > I just change the .in.data and CG-CG.dist.tgt file. >>>> >> >> >> >> >> >> > When I try to run this (even with the default spce.in >>>> >> >> >> >> >> >> > and spce.data file), I get this error: >>>> >> >> >> >> >> >> > sh run.sh >>>> >> >> >> >> >> >> > running csg_inverse --options "settings.xml" >>>> >> >> >> >> >> >> > Appending to existing logfile inverse.log >>>> >> >> >> >> >> >> > We are doing Method: ibi >>>> >> >> >> >> >> >> > Prepare (dir step_000) >>>> >> >> >> >> >> >> > Using initial guess from dist CG-CG.dist.tgt for CG-CG >>>> >> >> >> >> >> >> > step 0 done >>>> >> >> >> >> >> >> > Doing iteration 1 (dir step_001) >>>> >> >> >> >> >> >> > Simulation with lammps >>>> >> >> >> >> >> >> > ################################################################################################################################################ >>>> >> >> >> >> >> >> > # >>>> >> >> >> >> >> >> > >>>> >> >> >> >> >> >> > # >>>> >> >> >> >> >> >> > # ERROR: >>>> >> >> >> >> >> >> > >>>> >> >> >> >> >> >> > # >>>> >> >> >> >> >> >> > # Command/function lmp not found (when calling from >>>> >> >> >> >> >> >> > csg_call you might need to add --simprog option or set >>>> >> >> >> >> >> >> > cg.inverse.program in the xml file) # >>>> >> >> >> >> >> >> > # For details see the logfile >>>> >> >> >> >> >> >> > /ccs/home/rdguha/votca/csg-tutorials/spce/ibi_lammps/inverse.log >>>> >> >> >> >> >> >> > # >>>> >> >> >> >> >> >> > # >>>> >> >> >> >> >> >> > >>>> >> >> >> >> >> >> > # >>>> >> >> >> >> >> >> > ################################################################################################################################################ >>>> >> >> >> >> >> >> > run.sh: line 4: 2698557 Terminated >>>> >> >> >> >> >> >> > csg_inverse --options settings.xml >>>> >> >> >> >> >> >> > >>>> >> >> >> >> >> >> > I have attached the settings.xml file with this email. >>>> >> >> >> >> >> >> > Do you know what I have to change and where for lammps >>>> >> >> >> >> >> >> > to work? >>>> >> >> >> >> >> >> The error says it all, the lammps executable ("lmp") was >>>> >> >> >> >> >> >> not found, >>>> >> >> >> >> >> >> hence it stopped. >>>> >> >> >> >> >> >> >>>> >> >> >> >> >> >> You can change the lammps default name at cmake time >>>> >> >> >> >> >> >> using the >>>> >> >> >> >> >> >> LMP_EXECUTABLE option. >>>> >> >> >> >> >> >> Alternatively you can set the cg.inverse.lammps.command >>>> >> >> >> >> >> >> in your xml file. >>>> >> >> >> >> >> >> >>>> >> >> >> >> >> >> Christoph >>>> >> >> >> >> >> >> >>>> >> >> >> >> >> >> > >>>> >> >> >> >> >> >> > Thanks >>>> >> >> >> >> >> >> > >>>> >> >> >> >> >> >> > On Thu, Jul 8, 2021 at 12:43 PM Christoph Junghans >>>> >> >> >> >> >> >> > <[email protected]> wrote: >>>> >> >> >> >> >> >> >> >>>> >> >> >> >> >> >> >> On Thu, Jul 8, 2021 at 9:19 AM Rishabh Guha >>>> >> >> >> >> >> >> >> <[email protected]> wrote: >>>> >> >> >> >> >> >> >> > >>>> >> >> >> >> >> >> >> > I think there is an inconsistency here because >>>> >> >> >> >> >> >> >> > these coordinates are straight from my LAMMPS data >>>> >> >> >> >> >> >> >> > file:- >>>> >> >> >> >> >> >> >> > I have 500 beads in 500 molecules for the >>>> >> >> >> >> >> >> >> > coarsegraining >>>> >> >> >> >> >> >> >> > > -20.153 >>>> >> >> >> >> >> >> >> > > 0.534 >>>> >> >> >> >> >> >> >> > > -24.577 -18.68 >>>> >> >> >> >> >> >> >> > > 3.621 >>>> >> >> >> >> >> >> >> > > -23.916 >>>> >> >> >> >> >> >> >> > > an error occurred: >>>> >> >> >> >> >> >> >> > > coarse-grained bead is bigger than half the box >>>> >> >> >> >> >> >> >> > > (atoms N1 (id 18), O7 (id 22) , molecule 1). >>>> >> >> >> >> >> >> >> > >>>> >> >> >> >> >> >> >> > 18 1 1 -0.9187999963760376 -20.153000 0.534000 >>>> >> >> >> >> >> >> >> > -24.577000 >>>> >> >> >> >> >> >> >> > 22 1 7 -0.4959999918937683 -18.680000 3.621000 >>>> >> >> >> >> >> >> >> > -23.916000 >>>> >> >> >> >> >> >> >> > >>>> >> >> >> >> >> >> >> > Therefore, these are in Angstrom (not nm). So 3.621 >>>> >> >> >> >> >> >> >> > - 0.534 is technically 0.3087 nm. Not sure why >>>> >> >> >> >> >> >> >> > Votca is not doing the nm conversion here. >>>> >> >> >> >> >> >> >> You are right, I made a fix here: >>>> >> >> >> >> >> >> >> https://github.com/votca/csg/pull/697. We fixed it in >>>> >> >> >> >> >> >> >> the dump reader >>>> >> >> >> >> >> >> >> before, but seem to have missed it in the LAMMPS data >>>> >> >> >> >> >> >> >> reader. >>>> >> >> >> >> >> >> >> >>>> >> >> >> >> >> >> >> > >>>> >> >> >> >> >> >> >> > Anyways, I tried visualizing the .gro file in VMD >>>> >> >> >> >> >> >> >> > and it looks fine. Nothing stands out. The initial >>>> >> >> >> >> >> >> >> > file was 250 molecules of 2 different types of >>>> >> >> >> >> >> >> >> > amino acids. Since I mapped each molecule to a >>>> >> >> >> >> >> >> >> > single bead I now get 2 different types of beads >>>> >> >> >> >> >> >> >> > each being 250 in number. >>>> >> >> >> >> >> >> >> > >>>> >> >> >> >> >> >> >> > Can you please give me some pointers on how I >>>> >> >> >> >> >> >> >> > proceed now. My aim is to generate a CG potential >>>> >> >> >> >> >> >> >> > for these amino acid pairs based on RDF calculated >>>> >> >> >> >> >> >> >> > from the atomistic trajectories. I have already >>>> >> >> >> >> >> >> >> > calculated the RDF's from the atomistic trajectory >>>> >> >> >> >> >> >> >> > but I don't know how I use it in VOTCA. >>>> >> >> >> >> >> >> >> >>>> >> >> >> >> >> >> >> The csg manual has more details here: >>>> >> >> >> >> >> >> >> https://www.votca.org/csg/index.html >>>> >> >> >> >> >> >> >> But in short, you will have to generate input files >>>> >> >> >> >> >> >> >> for Gromacs (or >>>> >> >> >> >> >> >> >> LAMMPS) that have everything but the potentials. >>>> >> >> >> >> >> >> >> csg_gmxtopol can be a good starting point even though >>>> >> >> >> >> >> >> >> it can only deal >>>> >> >> >> >> >> >> >> with one type of molecule, but I usually start with >>>> >> >> >> >> >> >> >> one of the >>>> >> >> >> >> >> >> >> tutorials go from there, if you have 2 kinds of >>>> >> >> >> >> >> >> >> molecules, have a look >>>> >> >> >> >> >> >> >> at the methanol-water or urea-water tutorials: >>>> >> >> >> >> >> >> >> https://github.com/votca/csg-tutorials >>>> >> >> >> >> >> >> >> >>>> >> >> >> >> >> >> >> Christoph >>>> >> >> >> >> >> >> >> >>>> >> >> >> >> >> >> >> > >>>> >> >> >> >> >> >> >> > I was trying to follow some discussion topics on >>>> >> >> >> >> >> >> >> > the group and one of them mentions generating a CG >>>> >> >> >> >> >> >> >> > topology file using cg_gmxtopol. When I try that I >>>> >> >> >> >> >> >> >> > am getting this warning :- >>>> >> >> >> >> >> >> >> > >>>> >> >> >> >> >> >> >> > csg_gmxtopol --top topology.xml --cg >>>> >> >> >> >> >> >> >> > "lysine.xml;methionine.xml" --out topol.top >>>> >> >> >> >> >> >> >> > >>>> >> >> >> >> >> >> >> > 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 11000 beads in 500 molecules >>>> >> >> >> >> >> >> >> > I have 500 beads in 500 molecules for the >>>> >> >> >> >> >> >> >> > coarsegraining >>>> >> >> >> >> >> >> >> > WARNING: cannot create topology for topology >>>> >> >> >> >> >> >> >> > withmultiple molecules, using only first molecule >>>> >> >> >> >> >> >> >> > >>>> >> >> >> >> >> >> >> > >>>> >> >> >> >> >> >> >> > >>>> >> >> >> >> >> >> >> > On Thu, Jul 8, 2021 at 11:05 AM Christoph Junghans >>>> >> >> >> >> >> >> >> > <[email protected]> wrote: >>>> >> >> >> >> >> >> >> >> >>>> >> >> >> >> >> >> >> >> On Thu, Jul 8, 2021 at 8:21 AM Rishabh Guha >>>> >> >> >> >> >> >> >> >> <[email protected]> wrote: >>>> >> >> >> >> >> >> >> >> > >>>> >> >> >> >> >> >> >> >> > Hey Christoph, >>>> >> >> >> >> >> >> >> >> > >>>> >> >> >> >> >> >> >> >> > First of all thanks for following up. Sorry this >>>> >> >> >> >> >> >> >> >> > is gonna be a long email but I have some >>>> >> >> >> >> >> >> >> >> > interesting observations based on your question. >>>> >> >> >> >> >> >> >> >> > First of all if I try to do a topology dump >>>> >> >> >> >> >> >> >> >> > using my pdb file I don't get a "size" of the >>>> >> >> >> >> >> >> >> >> > box per say. >>>> >> >> >> >> >> >> >> >> > >>>> >> >> >> >> >> >> >> >> > I get this :- I have 8000 beads in 500 molecules >>>> >> >> >> >> >> >> >> >> > Boundary Condition: open >>>> >> >> >> >> >> >> >> >> > >>>> >> >> >> >> >> >> >> >> > Moreover the charges on my atoms are also 0 in >>>> >> >> >> >> >> >> >> >> > the pdb file. I figured that for my case, using >>>> >> >> >> >> >> >> >> >> > the LAMMPS data file I generate from my PDB file >>>> >> >> >> >> >> >> >> >> > is a better candidate. When I use the LAMMPS >>>> >> >> >> >> >> >> >> >> > data file, the identifiers change from 1:ALA:XX >>>> >> >> >> >> >> >> >> >> > to 1:DUM:XX. I did all those changes and then if >>>> >> >> >> >> >> >> >> >> > I do csg_dump I get:- >>>> >> >> >> >> >> >> >> >> > >>>> >> >> >> >> >> >> >> >> > I have 11000 beads in 500 molecules >>>> >> >> >> >> >> >> >> >> > Boundary Condition: orthorhombic >>>> >> >> >> >> >> >> >> >> > Box matix: 5.76509 0 0 >>>> >> >> >> >> >> >> >> >> > 0 5.76509 0 >>>> >> >> >> >> >> >> >> >> > 0 0 5.76509 (It was a different data >>>> >> >> >> >> >> >> >> >> > set which has 11000 molecules instead of 8000 so >>>> >> >> >> >> >> >> >> >> > that is not an issue) >>>> >> >> >> >> >> >> >> >> > >>>> >> >> >> >> >> >> >> >> > Now my original LAMMPS data file actually gies >>>> >> >> >> >> >> >> >> >> > from: >>>> >> >> >> >> >> >> >> >> > -28.825434 28.825434 xlo xhi >>>> >> >> >> >> >> >> >> >> > -28.825434 28.825434 ylo yhi >>>> >> >> >> >> >> >> >> >> > -28.825434 28.825434 zlo zhi >>>> >> >> >> >> >> >> >> >> > >>>> >> >> >> >> >> >> >> >> > So I guess VOTCA doesn't account for the >>>> >> >> >> >> >> >> >> >> > negative coordinates and starts everything from >>>> >> >> >> >> >> >> >> >> > 0. >>>> >> >> >> >> >> >> >> >> Well, 2x 28.825434 Angstroem = 5.76509 nm, so >>>> >> >> >> >> >> >> >> >> above it is correct. >>>> >> >> >> >> >> >> >> >> VOTCA uses minimum image convention when a box is >>>> >> >> >> >> >> >> >> >> given, so it is able >>>> >> >> >> >> >> >> >> >> deal with negative coordinates. >>>> >> >> >> >> >> >> >> >> >>>> >> >> >> >> >> >> >> >> > >>>> >> >> >> >> >> >> >> >> > I tried csg_map with this and I again got the >>>> >> >> >> >> >> >> >> >> > previous error: >>>> >> >> >> >> >> >> >> >> > I have 11000 beads in 500 molecules >>>> >> >> >> >> >> >> >> >> > I have 500 beads in 500 molecules for the >>>> >> >> >> >> >> >> >> >> > coarsegraining >>>> >> >> >> >> >> >> >> >> > -20.153 >>>> >> >> >> >> >> >> >> >> > 0.534 >>>> >> >> >> >> >> >> >> >> > -24.577 -18.68 >>>> >> >> >> >> >> >> >> >> > 3.621 >>>> >> >> >> >> >> >> >> >> > -23.916 >>>> >> >> >> >> >> >> >> >> > an error occurred: >>>> >> >> >> >> >> >> >> >> > coarse-grained bead is bigger than half the box >>>> >> >> >> >> >> >> >> >> > (atoms N1 (id 18), O7 (id 22) , molecule 1). >>>> >> >> >> >> >> >> >> >> Half box length 2.88254 nm, but | 3.621 - 0.534 | >>>> >> >> >> >> >> >> >> >> (y difference of the >>>> >> >> >> >> >> >> >> >> two beads above) is 3.087nm and hence bigger than >>>> >> >> >> >> >> >> >> >> L/2, so the error >>>> >> >> >> >> >> >> >> >> message is correct as well. >>>> >> >> >> >> >> >> >> >> >>>> >> >> >> >> >> >> >> >> > >>>> >> >> >> >> >> >> >> >> > This time around I just increased the box size >>>> >> >> >> >> >> >> >> >> > by a multiplier of 10 in x,y and z and it worked: >>>> >> >> >> >> >> >> >> >> > >>>> >> >> >> >> >> >> >> >> > 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 11000 beads in 500 molecules >>>> >> >> >> >> >> >> >> >> > I have 500 beads in 500 molecules for the >>>> >> >> >> >> >> >> >> >> > coarsegraining >>>> >> >> >> >> >> >> >> >> > Reading frame, timestep 5000000 >>>> >> >> >> >> >> >> >> >> > writing coarse-grained trajectory to cg.gro >>>> >> >> >> >> >> >> >> >> > >>>> >> >> >> >> >> >> >> >> > I wanted to know whether increasing the box size >>>> >> >> >> >> >> >> >> >> > is okay in this case. >>>> >> >> >> >> >> >> >> >> When you increase the box size you basically force >>>> >> >> >> >> >> >> >> >> the atoms in the >>>> >> >> >> >> >> >> >> >> 1st image of the periodic box. >>>> >> >> >> >> >> >> >> >> One problem with this method is that one could >>>> >> >> >> >> >> >> >> >> construct a case where >>>> >> >> >> >> >> >> >> >> a molecule would be broken into 2 pieces, when >>>> >> >> >> >> >> >> >> >> some atoms have >>>> >> >> >> >> >> >> >> >> coordinates on a different image than other atoms. >>>> >> >> >> >> >> >> >> >> Only way to know is >>>> >> >> >> >> >> >> >> >> to look at the output with vmd or pymol. >>>> >> >> >> >> >> >> >> >> >>>> >> >> >> >> >> >> >> >> Christoph >>>> >> >> >> >> >> >> >> >> > >>>> >> >> >> >> >> >> >> >> > Thanks again >>>> >> >> >> >> >> >> >> >> > >>>> >> >> >> >> >> >> >> >> > On Wed, Jul 7, 2021 at 6:35 PM Christoph >>>> >> >> >> >> >> >> >> >> > Junghans <[email protected]> wrote: >>>> >> >> >> >> >> >> >> >> >> >>>> >> >> >> >> >> >> >> >> >> On Wed, Jul 7, 2021 at 2:18 PM Rishabh Guha >>>> >> >> >> >> >> >> >> >> >> <[email protected]> wrote: >>>> >> >> >> >> >> >> >> >> >> > >>>> >> >> >> >> >> >> >> >> >> > Hey Christoph, >>>> >> >> >> >> >> >> >> >> >> > >>>> >> >> >> >> >> >> >> >> >> > First of all in my pdb file the atoms are at:- >>>> >> >> >> >> >> >> >> >> >> > ATOM 1 CA ALA A 1 11.853 >>>> >> >> >> >> >> >> >> >> >> > -2.654 0.787 1.00 0.00 C >>>> >> >> >> >> >> >> >> >> >> > ATOM 2 C ALA A 1 12.896 >>>> >> >> >> >> >> >> >> >> >> > -2.967 -0.276 1.00 0.00 C >>>> >> >> >> >> >> >> >> >> >> > >>>> >> >> >> >> >> >> >> >> >> > Do you know why votca is dividing all the >>>> >> >> >> >> >> >> >> >> >> > positions by 10? >>>> >> >> >> >> >> >> >> >> >> VOTCA uses nm internally, and pdb is in >>>> >> >> >> >> >> >> >> >> >> Angstrom. >>>> >> >> >> >> >> >> >> >> >> > >>>> >> >> >> >> >> >> >> >> >> > Secondly these atoms show up as- >>>> >> >> >> >> >> >> >> >> >> > 0 Name 1:ALA:CA Type CA Mass 12.0107 Resnr 0 >>>> >> >> >> >> >> >> >> >> >> > Resname ALA Charge 0 >>>> >> >> >> >> >> >> >> >> >> > 1 Name 1:ALA:C Type C Mass 12.0107 Resnr 0 >>>> >> >> >> >> >> >> >> >> >> > Resname ALA Charge 0 >>>> >> >> >> >> >> >> >> >> >> > when I do csg_dump --top topology.xml and are >>>> >> >> >> >> >> >> >> >> >> > mapped as 1:ALA:CA 1:ALA:C 1:ALA:N 1:ALA:H1 >>>> >> >> >> >> >> >> >> >> >> > 1:ALA:H2 1:ALA:CB 1:ALA:HA 1:ALA:HB1 >>>> >> >> >> >> >> >> >> >> >> > 1:ALA:HB2 1:ALA:HB3 1:ALA:O 1:ALA:OXT >>>> >> >> >> >> >> >> >> >> >> > 1:ALA:HXT in the alanine.xml file. >>>> >> >> >> >> >> >> >> >> >> > >>>> >> >> >> >> >> >> >> >> >> > I do not see any issues in the mapping to be >>>> >> >> >> >> >> >> >> >> >> > honest >>>> >> >> >> >> >> >> >> >> >> When you run csg_dump, what does it tell you >>>> >> >> >> >> >> >> >> >> >> the box size is? >>>> >> >> >> >> >> >> >> >> >> >>>> >> >> >> >> >> >> >> >> >> Christoph >>>> >> >> >> >> >> >> >> >> >> > >>>> >> >> >> >> >> >> >> >> >> > Regards >>>> >> >> >> >> >> >> >> >> >> > >>>> >> >> >> >> >> >> >> >> >> > On Wed, Jul 7, 2021 at 4:09 PM Christoph >>>> >> >> >> >> >> >> >> >> >> > Junghans <[email protected]> wrote: >>>> >> >> >> >> >> >> >> >> >> >> >>>> >> >> >> >> >> >> >> >> >> >> >>>> >> >> >> >> >> >> >> >> >> >> >>>> >> >> >> >> >> >> >> >> >> >> On Wed, Jul 7, 2021, 14:05 Rishabh Guha >>>> >> >> >> >> >> >> >> >> >> >> <[email protected]> wrote: >>>> >> >> >> >> >> >> >> >> >> >>> >>>> >> >> >> >> >> >> >> >> >> >>> Hey Christoph, >>>> >> >> >> >> >> >> >> >> >> >>> >>>> >> >> >> >> >> >> >> >> >> >>> Thanks for the pointers. I tried to look >>>> >> >> >> >> >> >> >> >> >> >>> closely into my mapping files and compared >>>> >> >> >> >> >> >> >> >> >> >>> them with the pdb files, but nothing jumped >>>> >> >> >> >> >> >> >> >> >> >>> out at me. Although I admit that it can >>>> >> >> >> >> >> >> >> >> >> >>> easily be an oversight-I have just started >>>> >> >> >> >> >> >> >> >> >> >>> using Votca today. I have attached all my >>>> >> >> >> >> >> >> >> >> >> >>> files below. Does anything jump out at you? >>>> >> >> >> >> >> >> >> >> >> >>> I am convinced that none of my atoms are >>>> >> >> >> >> >> >> >> >> >> >>> than half the box length away >>>> >> >> >> >> >> >> >> >> >> >> >>>> >> >> >> >> >> >> >> >> >> >> The error says there is an atom at 1.1853 >>>> >> >> >> >> >> >> >> >> >> >> -0.2654 0.0787 and one at 1.2896 -0.2967 >>>> >> >> >> >> >> >> >> >> >> >> -0.0276 that you are trying to map in a cg >>>> >> >> >> >> >> >> >> >> >> >> bead. These are the ones you have to look at >>>> >> >> >> >> >> >> >> >> >> >> carefully in the mapping file. >>>> >> >> >> >> >> >> >> >> >> >> >>>> >> >> >> >> >> >> >> >> >> >> Christoph >>>> >> >> >> >> >> >> >> >> >> >> >>>> >> >> >> >> >> >> >> >> >> >>> >>>> >> >> >> >> >> >> >> >> >> >>> >>>> >> >> >> >> >> >> >> >> >> >>> Regards >>>> >> >> >> >> >> >> >> >> >> >>> >>>> >> >> >> >> >> >> >> >> >> >>> On Wed, Jul 7, 2021 at 3:55 PM Christoph >>>> >> >> >> >> >> >> >> >> >> >>> Junghans <[email protected]> wrote: >>>> >> >> >> >> >> >> >> >> >> >>>> >>>> >> >> >> >> >> >> >> >> >> >>>> >>>> >> >> >> >> >> >> >> >> >> >>>> >>>> >> >> >> >> >> >> >> >> >> >>>> On Wed, Jul 7, 2021 at 13:44 Rishabh Guha >>>> >> >> >> >> >> >> >> >> >> >>>> <[email protected]> wrote: >>>> >> >> >> >> >> >> >> >> >> >>>>> >>>> >> >> >> >> >> >> >> >> >> >>>>> Hey Christoph, >>>> >> >> >> >> >> >> >> >> >> >>>>> >>>> >> >> >> >> >> >> >> >> >> >>>>> Thanks for the help. I got to know about >>>> >> >> >> >> >> >> >> >> >> >>>>> the csg_dump command as soon as I sent >>>> >> >> >> >> >> >> >> >> >> >>>>> you the email. For some reason, csg_dump >>>> >> >> >> >> >> >> >> >> >> >>>>> is categorizing all the atoms as the >>>> >> >> >> >> >> >> >> >> >> >>>>> valine molecules as ALA as well, which is >>>> >> >> >> >> >> >> >> >> >> >>>>> counterintuitive to me. >>>> >> >> >> >> >> >> >> >> >> >>>> >>>> >> >> >> >> >> >> >> >> >> >>>> yeah, there is a way to fix this, these >>>> >> >> >> >> >> >> >> >> >> >>>> are just unique identifiers so it doesn’t >>>> >> >> >> >> >> >> >> >> >> >>>> matter a lot what they are as long as they >>>> >> >> >> >> >> >> >> >> >> >>>> are unique. This artifact mainly stems >>>> >> >> >> >> >> >> >> >> >> >>>> from the fact that the pdb format misses >>>> >> >> >> >> >> >> >> >> >> >>>> some molecule information. >>>> >> >> >> >> >> >> >> >> >> >>>> >>>> >> >> >> >> >> >> >> >> >> >>>> >>>> >> >> >> >> >> >> >> >> >> >>>> >>>> >> >> >> >> >> >> >> >> >> >>>>> But I did change my valine.xml file to:- >>>> >> >> >> >> >> >> >> >> >> >>>>> >>>> >> >> >> >> >> >> >> >> >> >>>>> <cg_molecule> >>>> >> >> >> >> >> >> >> >> >> >>>>> <name>VAL</name> >>>> >> >> >> >> >> >> >> >> >> >>>>> <ident>VAL</ident> >>>> >> >> >> >> >> >> >> >> >> >>>>> <topology> >>>> >> >> >> >> >> >> >> >> >> >>>>> <cg_beads> >>>> >> >> >> >> >> >> >> >> >> >>>>> <cg_bead> >>>> >> >> >> >> >> >> >> >> >> >>>>> <name>VAL</name> >>>> >> >> >> >> >> >> >> >> >> >>>>> <type>VAL</type> >>>> >> >> >> >> >> >> >> >> >> >>>>> <mapping>A</mapping> >>>> >> >> >> >> >> >> >> >> >> >>>>> <beads> >>>> >> >> >> >> >> >> >> >> >> >>>>> 1:ALA:CA 1:ALA:C 1:ALA:N >>>> >> >> >> >> >> >> >> >> >> >>>>> 1:ALA:H1 1:ALA:H2 1:ALA:CB 1:ALA:HA >>>> >> >> >> >> >> >> >> >> >> >>>>> 1:ALA:CG1 1:ALA:HG11 1:ALA:HG12 >>>> >> >> >> >> >> >> >> >> >> >>>>> 1:ALA:HG13 1:ALA:CG2 1:ALA:HB 1:ALA:HG21 >>>> >> >> >> >> >> >> >> >> >> >>>>> 1:ALA:HG22 1:ALA:HG23 1:ALA:O 1:ALA:OXT >>>> >> >> >> >> >> >> >> >> >> >>>>> 1:ALA:HXT >>>> >> >> >> >> >> >> >> >> >> >>>>> </beads> >>>> >> >> >> >> >> >> >> >> >> >>>>> </cg_bead> >>>> >> >> >> >> >> >> >> >> >> >>>>> </cg_beads> >>>> >> >> >> >> >> >> >> >> >> >>>>> </topology> >>>> >> >> >> >> >> >> >> >> >> >>>>> <maps> >>>> >> >> >> >> >> >> >> >> >> >>>>> <map> >>>> >> >> >> >> >> >> >> >> >> >>>>> <name>A</name> >>>> >> >> >> >> >> >> >> >> >> >>>>> <weights>12 12 14 1 1 12 1 12 1 1 1 >>>> >> >> >> >> >> >> >> >> >> >>>>> 12 1 1 1 1 16 16 1</weights> >>>> >> >> >> >> >> >> >> >> >> >>>>> </map> >>>> >> >> >> >> >> >> >> >> >> >>>>> </maps> >>>> >> >> >> >> >> >> >> >> >> >>>>> </cg_molecule> >>>> >> >> >> >> >> >> >> >> >> >>>>> >>>> >> >> >> >> >> >> >> >> >> >>>>> Now, I get a different error, >>>> >> >> >> >> >> >> >> >> >> >>>>> I have 8000 beads in 500 molecules >>>> >> >> >> >> >> >> >> >> >> >>>>> I have 500 beads in 500 molecules for the >>>> >> >> >> >> >> >> >> >> >> >>>>> coarsegraining >>>> >> >> >> >> >> >> >> >> >> >>>>> 1.1853 >>>> >> >> >> >> >> >> >> >> >> >>>>> -0.2654 >>>> >> >> >> >> >> >> >> >> >> >>>>> 0.0787 1.2896 >>>> >> >> >> >> >> >> >> >> >> >>>>> -0.2967 >>>> >> >> >> >> >> >> >> >> >> >>>>> -0.0276 >>>> >> >> >> >> >> >> >> >> >> >>>>> an error occurred: >>>> >> >> >> >> >> >> >> >> >> >>>>> coarse-grained bead is bigger than half >>>> >> >> >> >> >> >> >> >> >> >>>>> the box >>>> >> >> >> >> >> >> >> >> >> >>>>> (atoms CA (id 1), C (id 2) , molecule 1) >>>> >> >> >> >> >> >> >> >> >> >>>>> >>>> >> >> >> >> >> >> >> >> >> >>>>> Can you please tell me what I can change? >>>> >> >> >> >> >> >> >> >> >> >>>> >>>> >> >> >> >> >> >> >> >> >> >>>> this error means you are trying to map teo >>>> >> >> >> >> >> >> >> >> >> >>>> atoms that are more than half a box length >>>> >> >> >> >> >> >> >> >> >> >>>> away into one cg bead. The 6 number above >>>> >> >> >> >> >> >> >> >> >> >>>> are the positions. >>>> >> >> >> >> >> >> >> >> >> >>>> >>>> >> >> >> >> >> >> >> >> >> >>>> There can be multiple reasons for that >>>> >> >> >> >> >> >> >> >> >> >>>> error, most of the times it is a typo in >>>> >> >> >> >> >> >> >> >> >> >>>> the mapping file. If you are sure things >>>> >> >> >> >> >> >> >> >> >> >>>> are correct, you can always make the box >>>> >> >> >> >> >> >> >> >> >> >>>> bigger. >>>> >> >> >> >> >> >> >> >> >> >>>> >>>> >> >> >> >> >> >> >> >> >> >>>> Christoph >>>> >> >> >> >> >> >> >> >> >> >>>>> >>>> >> >> >> >> >> >> >> >> >> >>>>> >>>> >> >> >> >> >> >> >> >> >> >>>>> >>>> >> >> >> >> >> >> >> >> >> >>>>> On Wed, Jul 7, 2021 at 3:29 PM Christoph >>>> >> >> >> >> >> >> >> >> >> >>>>> Junghans <[email protected]> wrote: >>>> >> >> >> >> >> >> >> >> >> >>>>>> >>>> >> >> >> >> >> >> >> >> >> >>>>>> >>>> >> >> >> >> >> >> >> >> >> >>>>>> >>>> >> >> >> >> >> >> >> >> >> >>>>>> On Wed, Jul 7, 2021 at 13:23 Rishabh >>>> >> >> >> >> >> >> >> >> >> >>>>>> Guha <[email protected]> wrote: >>>> >> >> >> >> >> >> >> >> >> >>>>>>> >>>> >> >> >> >> >> >> >> >> >> >>>>>>> Hello, >>>> >> >> >> >> >> >> >> >> >> >>>>>>> >>>> >> >> >> >> >> >> >> >> >> >>>>>>> I have an atomistic system consisting >>>> >> >> >> >> >> >> >> >> >> >>>>>>> of 250 alanine and 250 valine >>>> >> >> >> >> >> >> >> >> >> >>>>>>> molecules. I am trying to use cg_map >>>> >> >> >> >> >> >> >> >> >> >>>>>>> using the pdb file and the LAMMPS >>>> >> >> >> >> >> >> >> >> >> >>>>>>> output trajectory, but I am getting an >>>> >> >> >> >> >> >> >> >> >> >>>>>>> error:- >>>> >> >> >> >> >> >> >> >> >> >>>>>>> cannot find: <1:VAL:CA> in VAL >>>> >> >> >> >> >> >> >> >> >> >>>>>>> an error occurred: >>>> >> >> >> >> >> >> >> >> >> >>>>>>> mapping error: molecule 1:VAL:CA does >>>> >> >> >> >> >> >> >> >> >> >>>>>>> not exist >>>> >> >> >> >> >> >> >> >> >> >>>>>> >>>> >> >> >> >> >> >> >> >> >> >>>>>> try to run “csg_dump --top topol.xml” >>>> >> >> >> >> >> >> >> >> >> >>>>>> and check how VOTCA labels things. >>>> >> >> >> >> >> >> >> >> >> >>>>>> >>>> >> >> >> >> >> >> >> >> >> >>>>>> Christoph >>>> >> >> >> >> >> >> >> >> >> >>>>>> >>>> >> >> >> >> >> >> >> >> >> >>>>>>> >>>> >> >> >> >> >> >> >> >> >> >>>>>>> My topology file looks like:- >>>> >> >> >> >> >> >> >> >> >> >>>>>>> <topology base="temp.pdb"> >>>> >> >> >> >> >> >> >> >> >> >>>>>>> <molecules> >>>> >> >> >> >> >> >> >> >> >> >>>>>>> <clear/> >>>> >> >> >> >> >> >> >> >> >> >>>>>>> <define name="ALA" first="1" >>>> >> >> >> >> >> >> >> >> >> >>>>>>> nbeads="13" nmols="250"/> >>>> >> >> >> >> >> >> >> >> >> >>>>>>> <define name="VAL" first="3251" >>>> >> >> >> >> >> >> >> >> >> >>>>>>> nbeads="19" nmols="250"/> >>>> >> >> >> >> >> >> >> >> >> >>>>>>> </molecules> >>>> >> >> >> >> >> >> >> >> >> >>>>>>> </topology> >>>> >> >> >> >> >> >> >> >> >> >>>>>>> >>>> >> >> >> >> >> >> >> >> >> >>>>>>> My individual alanine and valine xml >>>> >> >> >> >> >> >> >> >> >> >>>>>>> files are:- >>>> >> >> >> >> >> >> >> >> >> >>>>>>> Alanine- >>>> >> >> >> >> >> >> >> >> >> >>>>>>> <cg_molecule> >>>> >> >> >> >> >> >> >> >> >> >>>>>>> <name>ALA</name> >>>> >> >> >> >> >> >> >> >> >> >>>>>>> <ident>ALA</ident> >>>> >> >> >> >> >> >> >> >> >> >>>>>>> <topology> >>>> >> >> >> >> >> >> >> >> >> >>>>>>> <cg_beads> >>>> >> >> >> >> >> >> >> >> >> >>>>>>> <cg_bead> >>>> >> >> >> >> >> >> >> >> >> >>>>>>> <name>ALA</name> >>>> >> >> >> >> >> >> >> >> >> >>>>>>> <type>ALA</type> >>>> >> >> >> >> >> >> >> >> >> >>>>>>> <mapping>A</mapping> >>>> >> >> >> >> >> >> >> >> >> >>>>>>> <beads> >>>> >> >> >> >> >> >> >> >> >> >>>>>>> 1:ALA:CA 1:ALA:C 1:ALA:N >>>> >> >> >> >> >> >> >> >> >> >>>>>>> 1:ALA:H1 1:ALA:H2 1:ALA:CB 1:ALA:HA >>>> >> >> >> >> >> >> >> >> >> >>>>>>> 1:ALA:HB1 1:ALA:HB2 1:ALA:HB3 1:ALA:O >>>> >> >> >> >> >> >> >> >> >> >>>>>>> 1:ALA:OXT 1:ALA:HXT >>>> >> >> >> >> >> >> >> >> >> >>>>>>> </beads> >>>> >> >> >> >> >> >> >> >> >> >>>>>>> </cg_bead> >>>> >> >> >> >> >> >> >> >> >> >>>>>>> </cg_beads> >>>> >> >> >> >> >> >> >> >> >> >>>>>>> </topology> >>>> >> >> >> >> >> >> >> >> >> >>>>>>> <maps> >>>> >> >> >> >> >> >> >> >> >> >>>>>>> <map> >>>> >> >> >> >> >> >> >> >> >> >>>>>>> <name>A</name> >>>> >> >> >> >> >> >> >> >> >> >>>>>>> <weights>12 12 14 1 1 12 1 1 1 1 >>>> >> >> >> >> >> >> >> >> >> >>>>>>> 16 16 1</weights> >>>> >> >> >> >> >> >> >> >> >> >>>>>>> </map> >>>> >> >> >> >> >> >> >> >> >> >>>>>>> </maps> >>>> >> >> >> >> >> >> >> >> >> >>>>>>> </cg_molecule> >>>> >> >> >> >> >> >> >> >> >> >>>>>>> >>>> >> >> >> >> >> >> >> >> >> >>>>>>> Valine >>>> >> >> >> >> >> >> >> >> >> >>>>>>> <cg_molecule> >>>> >> >> >> >> >> >> >> >> >> >>>>>>> <name>VAL</name> >>>> >> >> >> >> >> >> >> >> >> >>>>>>> <ident>VAL</ident> >>>> >> >> >> >> >> >> >> >> >> >>>>>>> <topology> >>>> >> >> >> >> >> >> >> >> >> >>>>>>> <cg_beads> >>>> >> >> >> >> >> >> >> >> >> >>>>>>> <cg_bead> >>>> >> >> >> >> >> >> >> >> >> >>>>>>> <name>VAL</name> >>>> >> >> >> >> >> >> >> >> >> >>>>>>> <type>VAL</type> >>>> >> >> >> >> >> >> >> >> >> >>>>>>> <mapping>A</mapping> >>>> >> >> >> >> >> >> >> >> >> >>>>>>> <beads> >>>> >> >> >> >> >> >> >> >> >> >>>>>>> 1:VAL:CA 1:VAL:C 1:VAL:N >>>> >> >> >> >> >> >> >> >> >> >>>>>>> 1:VAL:H1 1:VAL:H2 1:VAL:CB 1:VAL:HA >>>> >> >> >> >> >> >> >> >> >> >>>>>>> 1:VAL:CG1 1:VAL:HG11 1:VAL:HG12 >>>> >> >> >> >> >> >> >> >> >> >>>>>>> 1:VAL:HG13 1:VAL:CG2 1:VAL:HB >>>> >> >> >> >> >> >> >> >> >> >>>>>>> 1:VAL:HG21 1:VAL:HG22 1:VAL:HG23 >>>> >> >> >> >> >> >> >> >> >> >>>>>>> 1:VAL:O 1:VAL:OXT 1:VAL:HXT >>>> >> >> >> >> >> >> >> >> >> >>>>>>> </beads> >>>> >> >> >> >> >> >> >> >> >> >>>>>>> </cg_bead> >>>> >> >> >> >> >> >> >> >> >> >>>>>>> </cg_beads> >>>> >> >> >> >> >> >> >> >> >> >>>>>>> </topology> >>>> >> >> >> >> >> >> >> >> >> >>>>>>> <maps> >>>> >> >> >> >> >> >> >> >> >> >>>>>>> <map> >>>> >> >> >> >> >> >> >> >> >> >>>>>>> <name>A</name> >>>> >> >> >> >> >> >> >> >> >> >>>>>>> <weights>12 12 14 1 1 12 1 12 1 1 >>>> >> >> >> >> >> >> >> >> >> >>>>>>> 1 12 1 1 1 1 16 16 1</weights> >>>> >> >> >> >> >> >> >> >> >> >>>>>>> </map> >>>> >> >> >> >> >> >> >> >> >> >>>>>>> </maps> >>>> >> >> >> >> >> >> >> >> >> >>>>>>> </cg_molecule> >>>> >> >> >> >> >> >> >> >> >> >>>>>>> >>>> >> >> >> >> >> >> >> >> >> >>>>>>> I have attached the pdb file for >>>> >> >> >> >> >> >> >> >> >> >>>>>>> further reference. >>>> >> >> >> >> >> >> >> >> >> >>>>>>> >>>> >> >> >> >> >> >> >> >> >> >>>>>>> Can anyone please help me with this? >>>> >> >> >> >> >> >> >> >> >> >>>>>>> >>>> >> >> >> >> >> >> >> >> >> >>>>>>> -- >>>> >> >> >> >> >> >> >> >> >> >>>>>>> Join us on Slack: >>>> >> >> >> >> >> >> >> >> >> >>>>>>> https://join.slack.com/t/votca/signup >>>> >> >> >> >> >> >> >> >> >> >>>>>>> --- >>>> >> >> >> >> >> >> >> >> >> >>>>>>> You received this message because you >>>> >> >> >> >> >> >> >> >> >> >>>>>>> are subscribed to the Google Groups >>>> >> >> >> >> >> >> >> >> >> >>>>>>> "votca" group. >>>> >> >> >> >> >> >> >> >> >> >>>>>>> To unsubscribe from this group and stop >>>> >> >> >> >> >> >> >> >> >> >>>>>>> receiving emails from it, send an email >>>> >> >> >> >> >> >> >> >> >> >>>>>>> to [email protected]. >>>> >> >> >> >> >> >> >> >> >> >>>>>>> To view this discussion on the web >>>> >> >> >> >> >> >> >> >> >> >>>>>>> visit >>>> >> >> >> >> >> >> >> >> >> >>>>>>> https://groups.google.com/d/msgid/votca/3c0b76f3-ff3a-4013-8b74-d366e1e9c865n%40googlegroups.com. >>>> >> >> >> >> >> >> >> >> >> >>>>>> >>>> >> >> >> >> >> >> >> >> >> >>>>>> -- >>>> >> >> >> >> >> >> >> >> >> >>>>>> Christoph Junghans >>>> >> >> >> >> >> >> >> >> >> >>>>>> Web: http://www.compphys.de >>>> >> >> >> >> >> >> >> >> >> >>>>>> >>>> >> >> >> >> >> >> >> >> >> >>>>>> -- >>>> >> >> >> >> >> >> >> >> >> >>>>>> Join us on Slack: >>>> >> >> >> >> >> >> >> >> >> >>>>>> https://join.slack.com/t/votca/signup >>>> >> >> >> >> >> >> >> >> >> >>>>>> --- >>>> >> >> >> >> >> >> >> >> >> >>>>>> >>>> >> >> >> >> >> >> >> >> >> >>>>>> You received this message because you >>>> >> >> >> >> >> >> >> >> >> >>>>>> are subscribed to a topic in the Google >>>> >> >> >> >> >> >> >> >> >> >>>>>> Groups "votca" group. >>>> >> >> >> >> >> >> >> >> >> >>>>>> To unsubscribe from this topic, visit >>>> >> >> >> >> >> >> >> >> >> >>>>>> https://groups.google.com/d/topic/votca/C3L0xhdUs6s/unsubscribe. >>>> >> >> >> >> >> >> >> >> >> >>>>>> To unsubscribe from this group and all >>>> >> >> >> >> >> >> >> >> >> >>>>>> its topics, send an email to >>>> >> >> >> >> >> >> >> >> >> >>>>>> [email protected]. >>>> >> >> >> >> >> >> >> >> >> >>>>>> To view this discussion on the web visit >>>> >> >> >> >> >> >> >> >> >> >>>>>> https://groups.google.com/d/msgid/votca/CAHG27e7WZfOD2xdHy1AWWob7zNtdr5cBpYydNGp0WmA9sfqO9w%40mail.gmail.com. >>>> >> >> >> >> >> >> >> >> >> >>>>> >>>> >> >> >> >> >> >> >> >> >> >>>>> >>>> >> >> >> >> >> >> >> >> >> >>>>> >>>> >> >> >> >> >> >> >> >> >> >>>>> -- >>>> >> >> >> >> >> >> >> >> >> >>>>> Rishabh Debraj Guha(PhD student) >>>> >> >> >> >> >> >> >> >> >> >>>>> >>>> >> >> >> >> >> >> >> >> >> >>>>> Graduate Research Assistant >>>> >> >> >> >> >> >> >> >> >> >>>>> Mechanical and Aerospace Engineering >>>> >> >> >> >> >> >> >> >> >> >>>>> North Carolina State University >>>> >> >> >> >> >> >> >> >> >> >>>>> Contact:- +1-347-205-2280 >>>> >> >> >> >> >> >> >> >> >> >>>>> >>>> >> >> >> >> >> >> >> >> >> >>>>> -- >>>> >> >> >> >> >> >> >> >> >> >>>>> Join us on Slack: >>>> >> >> >> >> >> >> >> >> >> >>>>> https://join.slack.com/t/votca/signup >>>> >> >> >> >> >> >> >> >> >> >>>>> --- >>>> >> >> >> >> >> >> >> >> >> >>>>> You received this message because you are >>>> >> >> >> >> >> >> >> >> >> >>>>> subscribed to the Google Groups "votca" >>>> >> >> >> >> >> >> >> >> >> >>>>> group. >>>> >> >> >> >> >> >> >> >> >> >>>>> To unsubscribe from this group and stop >>>> >> >> >> >> >> >> >> >> >> >>>>> receiving emails from it, send an email >>>> >> >> >> >> >> >> >> >> >> >>>>> to [email protected]. >>>> >> >> >> >> >> >> >> >> >> >>>>> To view this discussion on the web visit >>>> >> >> >> >> >> >> >> >> >> >>>>> https://groups.google.com/d/msgid/votca/CAFKQktCXqB_zefYDpusjSBnLkt%2B77vfkgnU-dovocsFsiiKUow%40mail.gmail.com. >>>> >> >> >> >> >> >> >> >> >> >>>> >>>> >> >> >> >> >> >> >> >> >> >>>> -- >>>> >> >> >> >> >> >> >> >> >> >>>> Christoph Junghans >>>> >> >> >> >> >> >> >> >> >> >>>> Web: http://www.compphys.de >>>> >> >> >> >> >> >> >> >> >> >>>> >>>> >> >> >> >> >> >> >> >> >> >>>> -- >>>> >> >> >> >> >> >> >> >> >> >>>> Join us on Slack: >>>> >> >> >> >> >> >> >> >> >> >>>> https://join.slack.com/t/votca/signup >>>> >> >> >> >> >> >> >> >> >> >>>> --- >>>> >> >> >> >> >> >> >> >> >> >>>> You received this message because you are >>>> >> >> >> >> >> >> >> >> >> >>>> subscribed to a topic in the Google Groups >>>> >> >> >> >> >> >> >> >> >> >>>> "votca" group. >>>> >> >> >> >> >> >> >> >> >> >>>> To unsubscribe from this topic, visit >>>> >> >> >> >> >> >> >> >> >> >>>> https://groups.google.com/d/topic/votca/C3L0xhdUs6s/unsubscribe. >>>> >> >> >> >> >> >> >> >> >> >>>> To unsubscribe from this group and all its >>>> >> >> >> >> >> >> >> >> >> >>>> topics, send an email to >>>> >> >> >> >> >> >> >> >> >> >>>> [email protected]. >>>> >> >> >> >> >> >> >> >> >> >>>> To view this discussion on the web visit >>>> >> >> >> >> >> >> >> >> >> >>>> https://groups.google.com/d/msgid/votca/CAHG27e6Kjvwxvv4suXuuqLSQ57AJeh_Vi-CepLi4A%3DXb9MmzWg%40mail.gmail.com. >>>> >> >> >> >> >> >> >> >> >> >>> >>>> >> >> >> >> >> >> >> >> >> >>> >>>> >> >> >> >> >> >> >> >> >> >>> >>>> >> >> >> >> >> >> >> >> >> >>> -- >>>> >> >> >> >> >> >> >> >> >> >>> Rishabh Debraj Guha(PhD student) >>>> >> >> >> >> >> >> >> >> >> >>> >>>> >> >> >> >> >> >> >> >> >> >>> Graduate Research Assistant >>>> >> >> >> >> >> >> >> >> >> >>> Mechanical and Aerospace Engineering >>>> >> >> >> >> >> >> >> >> >> >>> North Carolina State University >>>> >> >> >> >> >> >> >> >> >> >>> Contact:- +1-347-205-2280 >>>> >> >> >> >> >> >> >> >> >> >>> >>>> >> >> >> >> >> >> >> >> >> >>> -- >>>> >> >> >> >> >> >> >> >> >> >>> Join us on Slack: >>>> >> >> >> >> >> >> >> >> >> >>> https://join.slack.com/t/votca/signup >>>> >> >> >> >> >> >> >> >> >> >>> --- >>>> >> >> >> >> >> >> >> >> >> >>> You received this message because you are >>>> >> >> >> >> >> >> >> >> >> >>> subscribed to the Google Groups "votca" >>>> >> >> >> >> >> >> >> >> >> >>> group. >>>> >> >> >> >> >> >> >> >> >> >>> To unsubscribe from this group and stop >>>> >> >> >> >> >> >> >> >> >> >>> receiving emails from it, send an email to >>>> >> >> >> >> >> >> >> >> >> >>> [email protected]. >>>> >> >> >> >> >> >> >> >> >> >>> To view this discussion on the web visit >>>> >> >> >> >> >> >> >> >> >> >>> https://groups.google.com/d/msgid/votca/CAFKQktBEGaPFAtudiU20y7Y-0pwe1jS2XXnvShd0kyXvfBLuOQ%40mail.gmail.com. >>>> >> >> >> >> >> >> >> >> >> >> >>>> >> >> >> >> >> >> >> >> >> >> -- >>>> >> >> >> >> >> >> >> >> >> >> Join us on Slack: >>>> >> >> >> >> >> >> >> >> >> >> https://join.slack.com/t/votca/signup >>>> >> >> >> >> >> >> >> >> >> >> --- >>>> >> >> >> >> >> >> >> >> >> >> You received this message because you are >>>> >> >> >> >> >> >> >> >> >> >> subscribed to a topic in the Google Groups >>>> >> >> >> >> >> >> >> >> >> >> "votca" group. >>>> >> >> >> >> >> >> >> >> >> >> To unsubscribe from this topic, visit >>>> >> >> >> >> >> >> >> >> >> >> https://groups.google.com/d/topic/votca/C3L0xhdUs6s/unsubscribe. >>>> >> >> >> >> >> >> >> >> >> >> To unsubscribe from this group and all its >>>> >> >> >> >> >> >> >> >> >> >> topics, send an email to >>>> >> >> >> >> >> >> >> >> >> >> [email protected]. >>>> >> >> >> >> >> >> >> >> >> >> To view this discussion on the web visit >>>> >> >> >> >> >> >> >> >> >> >> https://groups.google.com/d/msgid/votca/CAHG27e4ypf5Po8_zKmhBSbSTW_xgGBu09Bmj6Nsh8KdQtYJN-Q%40mail.gmail.com. >>>> >> >> >> >> >> >> >> >> >> > >>>> >> >> >> >> >> >> >> >> >> > >>>> >> >> >> >> >> >> >> >> >> > >>>> >> >> >> >> >> >> >> >> >> > -- >>>> >> >> >> >> >> >> >> >> >> > Rishabh Debraj Guha(PhD student) >>>> >> >> >> >> >> >> >> >> >> > >>>> >> >> >> >> >> >> >> >> >> > Graduate Research Assistant >>>> >> >> >> >> >> >> >> >> >> > Mechanical and Aerospace Engineering >>>> >> >> >> >> >> >> >> >> >> > North Carolina State University >>>> >> >> >> >> >> >> >> >> >> > Contact:- +1-347-205-2280 >>>> >> >> >> >> >> >> >> >> >> > >>>> >> >> >> >> >> >> >> >> >> > -- >>>> >> >> >> >> >> >> >> >> >> > Join us on Slack: >>>> >> >> >> >> >> >> >> >> >> > https://join.slack.com/t/votca/signup >>>> >> >> >> >> >> >> >> >> >> > --- >>>> >> >> >> >> >> >> >> >> >> > You received this message because you are >>>> >> >> >> >> >> >> >> >> >> > subscribed to the Google Groups "votca" group. >>>> >> >> >> >> >> >> >> >> >> > To unsubscribe from this group and stop >>>> >> >> >> >> >> >> >> >> >> > receiving emails from it, send an email to >>>> >> >> >> >> >> >> >> >> >> > [email protected]. >>>> >> >> >> >> >> >> >> >> >> > To view this discussion on the web visit >>>> >> >> >> >> >> >> >> >> >> > https://groups.google.com/d/msgid/votca/CAFKQktBH-gARMiCQR%2BdJVudO95mHB5ZZkf6odZJDxmp6U2a-nQ%40mail.gmail.com. >>>> >> >> >> >> >> >> >> >> >> >>>> >> >> >> >> >> >> >> >> >> >>>> >> >> >> >> >> >> >> >> >> >>>> >> >> >> >> >> >> >> >> >> -- >>>> >> >> >> >> >> >> >> >> >> Christoph Junghans >>>> >> >> >> >> >> >> >> >> >> Web: http://www.compphys.de >>>> >> >> >> >> >> >> >> >> >> >>>> >> >> >> >> >> >> >> >> >> -- >>>> >> >> >> >> >> >> >> >> >> Join us on Slack: >>>> >> >> >> >> >> >> >> >> >> https://join.slack.com/t/votca/signup >>>> >> >> >> >> >> >> >> >> >> --- >>>> >> >> >> >> >> >> >> >> >> You received this message because you are >>>> >> >> >> >> >> >> >> >> >> subscribed to a topic in the Google Groups >>>> >> >> >> >> >> >> >> >> >> "votca" group. >>>> >> >> >> >> >> >> >> >> >> To unsubscribe from this topic, visit >>>> >> >> >> >> >> >> >> >> >> https://groups.google.com/d/topic/votca/C3L0xhdUs6s/unsubscribe. >>>> >> >> >> >> >> >> >> >> >> To unsubscribe from this group and all its >>>> >> >> >> >> >> >> >> >> >> topics, send an email to >>>> >> >> >> >> >> >> >> >> >> [email protected]. >>>> >> >> >> >> >> >> >> >> >> To view this discussion on the web visit >>>> >> >> >> >> >> >> >> >> >> https://groups.google.com/d/msgid/votca/CAHG27e58qQRPUVC07BnJTeMtkm5StheQQTxsSQsDo_fOQz8Lcw%40mail.gmail.com. >>>> >> >> >> >> >> >> >> >> > >>>> >> >> >> >> >> >> >> >> > >>>> >> >> >> >> >> >> >> >> > >>>> >> >> >> >> >> >> >> >> > -- >>>> >> >> >> >> >> >> >> >> > Rishabh Debraj Guha(PhD student) >>>> >> >> >> >> >> >> >> >> > >>>> >> >> >> >> >> >> >> >> > Graduate Research Assistant >>>> >> >> >> >> >> >> >> >> > Mechanical and Aerospace Engineering >>>> >> >> >> >> >> >> >> >> > North Carolina State University >>>> >> >> >> >> >> >> >> >> > Contact:- +1-347-205-2280 >>>> >> >> >> >> >> >> >> >> > >>>> >> >> >> >> >> >> >> >> > -- >>>> >> >> >> >> >> >> >> >> > Join us on Slack: >>>> >> >> >> >> >> >> >> >> > https://join.slack.com/t/votca/signup >>>> >> >> >> >> >> >> >> >> > --- >>>> >> >> >> >> >> >> >> >> > You received this message because you are >>>> >> >> >> >> >> >> >> >> > subscribed to the Google Groups "votca" group. >>>> >> >> >> >> >> >> >> >> > To unsubscribe from this group and stop >>>> >> >> >> >> >> >> >> >> > receiving emails from it, send an email to >>>> >> >> >> >> >> >> >> >> > [email protected]. >>>> >> >> >> >> >> >> >> >> > To view this discussion on the web visit >>>> >> >> >> >> >> >> >> >> > https://groups.google.com/d/msgid/votca/CAFKQktD6b4Tqy%3DMAY6bS1BFwiSiXjtpYeGZ0ffg7Y3QAVLjaXA%40mail.gmail.com. >>>> >> >> >> >> >> >> >> >> >>>> >> >> >> >> >> >> >> >> >>>> >> >> >> >> >> >> >> >> >>>> >> >> >> >> >> >> >> >> -- >>>> >> >> >> >> >> >> >> >> Christoph Junghans >>>> >> >> >> >> >> >> >> >> Web: http://www.compphys.de >>>> >> >> >> >> >> >> >> >> >>>> >> >> >> >> >> >> >> >> -- >>>> >> >> >> >> >> >> >> >> Join us on Slack: >>>> >> >> >> >> >> >> >> >> https://join.slack.com/t/votca/signup >>>> >> >> >> >> >> >> >> >> --- >>>> >> >> >> >> >> >> >> >> You received this message because you are >>>> >> >> >> >> >> >> >> >> subscribed to a topic in the Google Groups "votca" >>>> >> >> >> >> >> >> >> >> group. >>>> >> >> >> >> >> >> >> >> To unsubscribe from this topic, visit >>>> >> >> >> >> >> >> >> >> https://groups.google.com/d/topic/votca/C3L0xhdUs6s/unsubscribe. >>>> >> >> >> >> >> >> >> >> To unsubscribe from this group and all its topics, >>>> >> >> >> >> >> >> >> >> send an email to >>>> >> >> >> >> >> >> >> >> [email protected]. >>>> >> >> >> >> >> >> >> >> To view this discussion on the web visit >>>> >> >> >> >> >> >> >> >> https://groups.google.com/d/msgid/votca/CAHG27e7OFP%2B_yTA0BNk4q07NbGfdH29QOpi0PoQ%3DdOPon2kTYA%40mail.gmail.com. >>>> >> >> >> >> >> >> >> > >>>> >> >> >> >> >> >> >> > >>>> >> >> >> >> >> >> >> > >>>> >> >> >> >> >> >> >> > -- >>>> >> >> >> >> >> >> >> > Rishabh Debraj Guha(PhD student) >>>> >> >> >> >> >> >> >> > >>>> >> >> >> >> >> >> >> > Graduate Research Assistant >>>> >> >> >> >> >> >> >> > Mechanical and Aerospace Engineering >>>> >> >> >> >> >> >> >> > >> >> -- >> Christoph Junghans >> Web: http://www.compphys.de >> >> -- >> Join us on Slack: https://join.slack.com/t/votca/signup >> --- >> You received this message because you are subscribed to a topic in the >> Google Groups "votca" group. >> To unsubscribe from this topic, visit >> https://groups.google.com/d/topic/votca/C3L0xhdUs6s/unsubscribe. >> To unsubscribe from this group and all its topics, send an email to >> [email protected]. >> To view this discussion on the web visit >> https://groups.google.com/d/msgid/votca/CAHG27e5dgyOgWA0NzfbxCGOZ_AVVUz-CyB9fQGoRs-EbnTjfqw%40mail.gmail.com. > > > > -- > Rishabh Debraj Guha(PhD student) > > Graduate Research Assistant > Mechanical and Aerospace Engineering > North Carolina State University > Contact:- +1-347-205-2280 > > -- > Join us on Slack: https://join.slack.com/t/votca/signup > --- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To view this discussion on the web visit > https://groups.google.com/d/msgid/votca/CAFKQktDmssU84_hLUb-7VjitBhomuLxXOMvrj07uBwDTS%2BKnkg%40mail.gmail.com. -- Christoph Junghans Web: http://www.compphys.de -- Join us on Slack: https://join.slack.com/t/votca/signup --- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/votca/CAHG27e7%3DHwYoKG-bLPqF2eY%2B2jZ1HygTuEG9RikWTbaSkmSwVQ%40mail.gmail.com.
