.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 >> >> >> >> >> >> >> >> >>>>>>> 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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 >> >> >> >> >> >> > 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/CAFKQktB2v_gQSQxrnuwOk382V-N6FustzWs%3DoP8%3DY-A_0n2WRg%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/CAHG27e5AEia5NhbG3BPfb27Z2GTySAqoWR5BP%2BZX5edvimmjAQ%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/CAFKQktB25AKd9yfZ%3DfHDKDJA0ghNJwkhbmPuBK%3DDCz84tzwUdA%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/CAHG27e4rUc%3Ds%2BBY1mYkGo28L9OwDJ0Fr7iBH5Hu05Hx8eUOaEw%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/CAFKQktBmizoMbLLR3XLpse7cGE_q1GSOquqFHA2HDujSAB0xqQ%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/CAHG27e5T7jNC7Ntsfdf4y3KYz5-su6cKPrsi8u7R1E3u5a2bGw%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/CAFKQktBKMvOSzp-jaQ_q0Ewh0NdGS3K8baxx2RkA23Ga-QRL4g%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/CAHG27e5F350Jm8_JDZRhphAGz1EbsunP4Q9Ai_mf3-8R62Bthg%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/CAFKQktATu1ptirzBhrhX9ZsHr%2B7FkiizFYf%3DTd5gzQEZEWu8LQ%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/CAHG27e7zqoR2gzgzZxTkH1GQ%3D3k0U6-%2BoUr4Wor4G%3D_76w9ccg%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/CAFKQktDkNe0wt6%3D1pfe8twu6tu5WPCQWZamXVTqRD42GPfJDZw%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/CAHG27e7q20Y78TKTrz85xw7gBVBX05pLdPNTWbMxiwpP29yYiw%40mail.gmail.com. > > -- > 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/CAFKQktBUHP5ekDHJ3Qai%3DrNNyaj6%2BauijAiSs%2BV%2BcqA1R9A9WA%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/CAHG27e6QMWzUZh%2BcqsdxkD3xXX8aX7%2BDBFvT24q6vbJoh7H%3DJQ%40mail.gmail.com.
