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