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 moleculesBoundary 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. I tried csg_map with this and I again got the previous error: *I have 11000 beads in 500 moleculesI have 500 beads in 500 molecules for the coarsegraining-20.153 0.534-24.577 -18.68 3.621-23.916an error occurred:coarse-grained bead is bigger than half the box (atoms N1 (id 18), O7 (id 22) , molecule 1).* 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 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 coarsegrainingReading frame, timestep 5000000writing coarse-grained trajectory to cg.gro* I wanted to know whether increasing the box size is okay in this case. 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 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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. 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