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: >> >> >> 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>> >>>>> >> >> >> >> >> >> >> >>>>> 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 >> >> >> >> >> > 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 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/CAHG27e7q20Y78TKTrz85xw7gBVBX05pLdPNTWbMxiwpP29yYiw%40mail.gmail.com.
