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 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/CAHG27e7OFP%2B_yTA0BNk4q07NbGfdH29QOpi0PoQ%3DdOPon2kTYA%40mail.gmail.com.
