On Mon, Apr 6, 2020 at 2:52 PM Wolfgang Verestek < [email protected]> wrote:
> > Hi all, > > I've got a question about the rdf computation and the mapping file. I > wrote some python code to create the mapping files from a lammps data file. > Although there are several molecules i want to keep it to one mapping file > for convenience. Also the ordering is not the same inside different > molecules of the same type Instead I'm trying to use the residue IDs to > keep track of the molecules. > In the attached small example there are 4 molecules (1/2 short PA6 chains > and 3/4 two water molecules). : > Atom ID 1:79 PA6 #1 > Atom ID 80:158 PA6 #2 > Atom ID 159:161 Water #1 > Atom ID 162:164 Water #2 > So the first question is: Is this doable at all? OR am i misunderstanding > sth very basic here? > It should be doable, you will create two mapping files though. Mapping.cg.xml is ok, but will need a mapping.water.xml as well. One of each molecule type. > > the out put of 'csg_dump --top ../mapping.xml' looks ok to me. > I would call this file "topology.xml" not mapping. > I have 164 beads in 1 molecules > Boundary Condition: open > This might be the problem, try to add a line like <box xx="4.03100" yy="4.03100" zz="4.03100"/> to your topology file to define the box size. > > List of residues: > 0 name: m1AA id: 0 > 1 name: m1AA id: 1 > 2 name: m1AA id: 2 > 3 name: m1AA id: 3 > > List of molecules: > molecule: 1 m1AA beads: 164 > 0 Name 1:m1AA:1 Type 3 Mass 12.0112 Resnr 0 Resname m1AA Charge -0.106 > 1 Name 1:m1AA:2 Type 4 Mass 1.00797 Resnr 0 Resname m1AA Charge 0.053 > 2 Name 1:m1AA:3 Type 4 Mass 1.00797 Resnr 0 Resname m1AA Charge 0.053 > 3 Name 1:m1AA:4 Type 3 Mass 12.0112 Resnr 0 Resname m1AA Charge -0.106 > ... > 162 Name 1:m1AA:163 Type 11 Mass 1.00797 Resnr 3 Resname m1AA Charge 0.3991 > 163 Name 1:m1AA:164 Type 11 Mass 1.00797 Resnr 3 Resname m1AA Charge 0.3991 > > whereas 'csg_dump --top ../mapping.xml --cg ../mapping.cg.xml' shows that > the resID gets lost (But isn't absolutely necessary anyways i guess) . > I have 164 beads in 1 molecules > I have 18 beads in 1 molecules for the coarsegraining > Boundary Condition: open > > List of residues: > 0 name: m1CG id: 0 > > List of molecules: > molecule: 1 m1CG beads: 18 > 0 Name 1 Type 1 Mass 56.1084 Resnr 0 Resname m1CG Charge 0 > 1 Name 2 Type 2 Mass 57.0523 Resnr 0 Resname m1CG Charge 0 > ... > 16 Name 17 Type 5 Mass 18.0153 Resnr 0 Resname m1CG Charge 0 > 17 Name 18 Type 5 Mass 18.0153 Resnr 0 Resname m1CG Charge 0 > Is there a way to adjust the boundary condition and the Resnr for the CG > mapping? > See above for the box size, there is "resid" property in the topology file, but I don't think you can to it after the mapping. > > So i went on to check the RDF 'csg_stat --top ../mapping.xml --trj > ../chemistry.dump --options ../settings.xml --first-frame 0 --nframes 1' > which leads to the plot given the below (data also attached in the zip > file). By reading the all atom trajectory lammps snapshot and comparing the > results with Ovito output the results somehow match qualitatively, at least > in the beginning. for larger distances the decay somehow made me think that > periodic boundary conditions are not enforced (the lammps dump file is in > unwrapped coords). Is there a way to enforce periodic boundary conditions > and backmapping into the cell (or could this be the reason at all)? Should > i adjust the lammps dump file to have wrapped coords? Any other pitfalls i > might not have considered? > See above for the boundary cond. question, so that should solve that. I think the lammps interface is not as well used as the gromacs one, hence you will find some more pitfalls. Christoph > > > Regards > Wolfgang > > -- > 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/c8e63e00-48be-42db-8a77-de6e92dd11ef%40googlegroups.com > <https://groups.google.com/d/msgid/votca/c8e63e00-48be-42db-8a77-de6e92dd11ef%40googlegroups.com?utm_medium=email&utm_source=footer> > . > -- Christoph Junghans Web: http://www.compphys.de -- 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/CAHG27e6mziWkiK7fqH9gKw-qSqriX2gNy_9JX4AwN9NwcBSaDQ%40mail.gmail.com.
