Got it! Thank you so much! Best, J 在2024年4月4日星期四 UTC-5 08:53:28<Christoph Junghans> 写道：
> On Wed, Apr 3, 2024 at 5:28 PM 'JIANXIN HE' via votca > <[email protected]> wrote: > > > > Dear Christoph, > > > > Thank you for your clear explanation!!! I have successfully utilized > VOTCA for mapping LAMMPS (all atom) following your guidance, specifically > using the command: > > csg_map --top topol.xml --trj lammps.data --cg mapping.xml --out > lmp_cg.dump > > I have a small question regarding the output from --out lmp_cg.dump. Is > it possible to export this data back into a LAMMPS data file format? If so, > how can I specify the styles for the data file? I did not find detailed > instructions in the manual. > No, that is not implemented. > > > While using csg_dump --top lammps.data > log, I noticed a kind warning > indicating that the VOTCA LAMMPS data reader supports certain styles > (angle, atom, bond, full, molecule). > > Or it only --out the dump file? Thank you for your assistance. > That is correct, the lammps reader can only digest certain styles in > the input file. > > For both issues, patches are welcome, after all VOTCA is open-source. > > Christoph > > > > > Best, > > J. > > On Monday, February 21, 2022 at 4:50:12 PM UTC-6 Christoph Junghans > wrote: > >> > >> On Mon, Feb 21, 2022 at 3:08 PM Satyen Dhamankar <[email protected]> > wrote: > >> > > >> > Furthermore, where is the resname DUM coming from? > >> It is the residue name and as data file have no residue name, VOTCA > >> sets it to DUM for dummy. > >> > >> > > >> > On Monday, February 21, 2022 at 4:54:43 PM UTC-5 Satyen Dhamankar > wrote: > >> >> > >> >> Oh sorry for the misunderstanding. I have already run a SPCE > simulation in LAMMPS. I wanted to get the coarse-grained initial config > using csg_map, however, i am not sure how to go about making the > mapping.xml file using the current directions that you have. > >> >> > >> >> This is what I see when I run csg_dump --top sys.data, this is what > I see: > >> >> ``` > >> >> 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 2187 beads in 729 molecules > >> >> Boundary Condition: orthorhombic > >> >> Box matix: 2.8 0 0 > >> >> 0 2.8 0 > >> >> 0 0 2.8 > >> >> > >> >> List of residues: > >> >> 0 name: DUM id: 0 > >> >> 1 name: DUM id: 1 > >> >> 2 name: DUM id: 2 > >> >> 3 name: DUM id: 3 > >> >> 4 name: DUM id: 4 > >> >> 5 name: DUM id: 5 > >> >> 6 name: DUM id: 6 > >> >> 7 name: DUM id: 7 > >> >> 8 name: DUM id: 8 > >> >> 9 name: DUM id: 9 > >> >> ... > >> >> List of molecules: > >> >> molecule: 1 H2O1 beads: 3 > >> >> 0 Name O1 Type O1 Mass 15.9994 Resnr 0 Resname DUM Charge -0.82 > >> >> 1 Name H2 Type H2 Mass 1.008 Resnr 0 Resname DUM Charge 0.41 > >> >> 2 Name H2 Type H2 Mass 1.008 Resnr 0 Resname DUM Charge 0.41 > >> >> molecule: 2 H2O1 beads: 3 > >> >> 3 Name O1 Type O1 Mass 15.9994 Resnr 1 Resname DUM Charge -0.82 > >> >> 4 Name H2 Type H2 Mass 1.008 Resnr 1 Resname DUM Charge 0.41 > >> >> 5 Name H2 Type H2 Mass 1.008 Resnr 1 Resname DUM Charge 0.41 > >> >> molecule: 3 H2O1 beads: 3 > >> >> ... > >> >> ``` > >> >> Reading the above, molecule name is H2O1. What I dont get, is that > the H2 molecules are exactly the same, except for the sr no. If i have a > larger molecule without symmetric hydrogens, I imagine the program will not > be able to distinguish. How should I go about making the xml file? > >> I think for more complicated molecule, you will need to create xml > >> topology file. > >> See towards the end of > >> https://www.votca.org/csg/input_files.html#advanced-topology-handling. > >> > >> You can basically do something like: > >> $ cat topol.xml > >> <topology> > >> <molecules> > >> <box xx="2.8" yy="2.8" zz="2.8" /> > >> <molecule name="H20" nmols="729" nbeads="3"> > >> <!-- composition of molecule, bead definition --> > >> <bead name="O1" type="O" mass="15.9994" q="-0.82" /> > >> <bead name="H1" type="H" mass="1.008" q="0.41" /> > >> <bead name="H2" type="H" mass="1.008" q="0.41" /> > >> </molecule> > >> </topology> > >> then you can use H20:O1 etc in the mapping file. (Check with csg_dump > >> --top topol.xml first.) > >> > >> inferring all topology information from all different MD inputs is > >> sometimes incomplete, hence we have the xml topology format. > >> Patches for the lammps data reader are always welcome. > >> > >> >> This is what I have right now, > >> >> <cg_molecule> > >> >> <name>CG_WATER</name> > >> >> <ident>H2O1</ident> > >> >> <topology> > >> >> <cg_beads> > >> >> <cg_bead> > >> >> <name>b1</name> > >> >> <type>b</type> > >> >> <symmetry>1</symmetry> > >> >> <mapping>M1</mapping> > >> >> <beads> 1:H2O1:H2 1:H2O1:O1 1:H2O1:H2 </beads> > >> >> </cg_bead> > >> >> </cg_beads> > >> >> </topology> > >> >> <maps> > >> >> <map> > >> >> <name>M1</name> > >> >> <weights> 1 16 1</weights> > >> >> </map> > >> >> </maps> > >> >> </cg_molecule> > >> >> > >> >> When I run csg_map --top sys.data > >> >> 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 2187 beads in 729 molecules > >> >> cannot find: <1:H2O1:H2> in H2O1 > >> >> an error occurred: > >> >> mapping error: molecule 1:H2O1:H2 does not exist > >> >> > >> >> Where is the error taking place here? > >> Can you try "0:H2O1:H2" instead? > >> > >> >> On Monday, February 21, 2022 at 12:44:53 PM UTC-5 Christoph Junghans > wrote: > >> >>> > >> >>> On Mon, Feb 21, 2022 at 9:59 AM Satyen Dhamankar <[email protected]> > wrote: > >> >>> > > >> >>> > Hello, > >> >>> > > >> >>> > I believe this question has been asked quite a few times, but I > am still rather in the dark regarding this. How does one go from a LAMMPS > dump file to a coarse-grained trajectory? > >> >>> > > >> >>> > Much like the tutorials, I am running my own SPCE water > simulation. This is the form of my LAMMPS dump file: > >> >>> > ITEM: TIMESTEP > >> >>> > 111000 > >> >>> > ITEM: NUMBER OF ATOMS > >> >>> > 2187 > >> >>> > ITEM: BOX BOUNDS pp pp pp > >> >>> > -1.3011386691164584e-01 2.8130113866912254e+01 > >> >>> > -1.3011386691164584e-01 2.8130113866912254e+01 > >> >>> > -1.3011386691164584e-01 2.8130113866912254e+01 > >> >>> > ITEM: ATOMS id type mol xu yu zu > >> >>> > 1 1 1 15.9191 21.2231 7.26312 > >> >>> > 2 2 1 15.1846 20.9848 7.89853 > >> >>> > 3 2 1 15.9358 20.5644 6.51092 > >> >>> > 4 1 2 9.47096 4.06014 23.0485 > >> >>> > 5 2 2 9.95291 3.43993 23.6674 > >> >>> > 6 2 2 9.25497 4.90974 23.5296 > >> >>> > 7 1 3 -3.19525 17.8848 16.2274 > >> >>> > 8 2 3 -3.73498 18.5917 15.7703 > >> >>> > 9 2 3 -2.992 18.1735 17.163 > >> >>> > ... > >> >>> > Now, just looking at this trajectory, my molecule of water has no > name in particular. So, I am not sure what to put in the <ident> tag in the > water.xml file. In the spce tutorial, the csg_map command uses topol.tpr > for topology. But it does not seem like sys.data files which define a > lammps topology is accepted. > >> >>> > > >> >>> > This is my sys.data file: > >> >>> > 2187 atoms > >> >>> > 2 atom types > >> >>> > 1458 bonds > >> >>> > 1 bond types > >> >>> > 729 angles > >> >>> > 1 angle types > >> >>> > 0 dihedrals > >> >>> > 0 dihedral types > >> >>> > > >> >>> > 0.0000000000000000e+00 2.8000000000000000e+01 xlo xhi > >> >>> > 0.0000000000000000e+00 2.8000000000000000e+01 ylo yhi > >> >>> > 0.0000000000000000e+00 2.8000000000000000e+01 zlo zhi > >> >>> > > >> >>> > Masses > >> >>> > > >> >>> > 1 15.99940 # OSPCe > >> >>> > 2 1.00800 # HSPCe > >> >>> > > >> >>> > Atoms > >> >>> > > >> >>> > 1 1 1 -0.82000 26.4795641655 13.9845510766 10.8342774813 0 0 0 > >> >>> > 2 1 2 0.41000 26.0120845362 13.3829183164 11.4331512727 0 0 0 > >> >>> > 3 1 2 0.41000 26.3193693668 14.8622934936 11.2114417372 0 0 0 > >> >>> > 4 2 1 -0.82000 14.0145593114 1.5446899105 26.5086662016 0 0 0 > >> >>> > 5 2 2 0.41000 14.6271886820 1.6095611553 25.7605846713 0 0 0 > >> >>> > 6 2 2 0.41000 13.1417198035 1.6740140444 26.1089494746 0 0 0 > >> >>> > 7 3 1 -0.82000 4.6668218860 23.2721041307 17.0845511689 0 0 0 > >> >>> > > >> >>> > The pdb file I use to generate the water is: > >> >>> > COMPND UNNAMED > >> >>> > AUTHOR GENERATED BY OPEN BABEL 2.3.90 > >> >>> > HETATM 1 O HOH 1 0.154 1.797 0.015 1.00 0.00 OSPCe > >> >>> > HETATM 2 H HOH 0 1.122 1.767 -0.020 1.00 0.00 HSPCe > >> >>> > HETATM 3 H HOH 0 -0.125 1.206 -0.700 1.00 0.00 HSPCe > >> >>> > CONECT 1 2 3 > >> >>> > CONECT 2 1 > >> >>> > CONECT 3 1 > >> >>> > MASTER 0 0 0 0 0 0 0 0 3 0 3 0 > >> >>> > END > >> >>> > > >> >>> > How should one proceed with LAMMPS? Is there a specific way one > should set up topology in the event I have to run a CG simulation? > >> >>> I guess the first question is more for the lammps mailing list/ > >> >>> MatSci.org forum in the lammps section. They will know better how to > >> >>> run an SPCE simulation in LAMMPS. We provide input files for gromacs > >> >>> in the atomistic/ folder. If you are using the docker container you > >> >>> should have gromacs installed already. > >> >>> > >> >>> For the second question, to run a cg simulation you will need to > >> >>> create a cg initial condition, input settings file (settings.xml), > >> >>> target rdf and lammps script (in file) > >> >>> > >> >>> To generate the initial condition you can map an atomic file on a cg > >> >>> one using csg_map with a mapping file. (csg_map --top atomic.data > --cg > >> >>> mapping.xml --trj atomic.data --out cg.dump) > >> >>> > >> >>> The mapping file is something you need to write by hand or you can > use > >> >>> the stock tool (http://stock.cmm.ki.si/smt/). You can run csg_dump > >> >>> --top atomic.data to see what votca reads as molecule name and bead > >> >>> types to use in the mapping file. > >> >>> > >> >>> The target rdf you can calculate with csg_stat --top atomic.data > --cg > >> >>> mapping.xml --trj atomic_traj.dump --options settings.xml > >> >>> > >> >>> The csg manual (https://www.votca.org/csg/index.html) has a section > >> >>> about input files as well. > >> >>> > >> >>> Hope that helps, > >> >>> > >> >>> Christoph > >> >>> > > >> >>> > I would appreciate any advice you have for me. > >> >>> > > >> >>> > -- > >> >>> > 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/901cde37-475f-400e-92ed-df18ed63baden%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 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/34d4cee2-9505-46ea-9ea1-5c07f16c1cffn%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 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/95c7f44c-b6b5-4dd9-af72-826b2b1415f9n%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 the Google Groups "votca" group. 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