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. 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. 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.topWARNING: The votca lammps data reader is only able to read lammps files formatted in the following styles:angleatombondfullmoleculeThese styles use the following formats in the atom block:atom-ID molecule-ID atom-type charge x y zatom-ID molecule-ID atom-type charge x y z nx ny nzatom-ID molecule-ID atom-type x y zatom-ID molecule-ID atom-type x y z nx ny nzatom-ID atom-type x y zatom-ID atom-type x y z nx ny nzI have 11000 beads in 500 moleculesI have 500 beads in 500 molecules for the coarsegrainingWARNING: 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. 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