2014-11-14 5:35 GMT-07:00 Daniel Allen <[email protected]>: > Hi Christoph, thanks for the quick response. > > So I understand that there is no atomic mass information contained within a > pdb, that's fine. I also know that the values in the <weights> tag in the > --cg file aren't necessarily the real masses but are just relative weights > which end up being normalised in the mapping operator. > > My issue is that when I run: > > $ csg_dump --top topol.xml --cg PEO16-PBO22.xml > > for my system, the output looks like this: > > .................... > 12 Name PEO13 Type PEO Mass 7 Resnr 0 Resname PEO16-PBO22 > 13 Name PEO14 Type PEO Mass 7 Resnr 0 Resname PEO16-PBO22 > 14 Name PEO15 Type PEO Mass 7 Resnr 0 Resname PEO16-PBO22 > 15 Name PEO16 Type PEO Mass 7 Resnr 0 Resname PEO16-PBO22 > 16 Name PBO1 Type PBO Mass 13 Resnr 0 Resname PEO16-PBO22 > 17 Name PBO2 Type PBO Mass 13 Resnr 0 Resname PEO16-PBO22 > 18 Name PBO3 Type PBO Mass 13 Resnr 0 Resname PEO16-PBO22 > .................... > > where the mass is simply the number of atoms that are mapped to a bead. When > I go to the hexane tutorial and run: > > $csg_dump --top topol.tpr --cg hexane.xml > > the output is like so: > > ........................... > molecule: 996 HEX beads: 3 > 2985 Name A1 Type A Mass 29.062 Resnr 995 Resname HEX > 2986 Name B Type B Mass 28.054 Resnr 995 Resname HEX > 2987 Name A2 Type A Mass 29.062 Resnr 995 Resname HEX > molecule: 997 HEX beads: 3 > 2988 Name A1 Type A Mass 29.062 Resnr 996 Resname HEX > 2989 Name B Type B Mass 28.054 Resnr 996 Resname HEX > 2990 Name A2 Type A Mass 29.062 Resnr 996 Resname HEX > molecule: 998 HEX beads: 3 > 2991 Name A1 Type A Mass 29.062 Resnr 997 Resname HEX > 2992 Name B Type B Mass 28.054 Resnr 997 Resname HEX > 2993 Name A2 Type A Mass 29.062 Resnr 997 Resname HEX > .......................... > > In this case, the mass for each CG bead is the sum of the atomic masses of > the atoms that form the bead. Is that simply because the masses are > contained in a gromacs topology file? Yes, a tpr file contains mass information. As I said in my last email you can use the <mass> tag in topol.xml to change the masses.
> > > > Can I be confident that a centre of mass mapping is used when running > csg_map for my system? Map a single frame (e.g. your pdb file) using csg_map and look at the output. E.g. in VMD one can show them on top of each other. However, as Eqn 2.5 doesn't contain masses the mapping should be fine. But remember, mapped velocity (does not apply for a pdb files as they don't contain velocities) will be wrong. > > I know that the masses don't affect thermodynamic quantities but they're > important for bonded interactions right because the position of the CG bead > will be wrong if the masses of all atoms are weighted equally. I am not sure I understand your comment, Eqn. 2.5 doesn't contain masses, so the position of the CG bead won't change for different mass values. Christoph > > Cheers, Dan. > > -- > 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 post to this group, send email to [email protected]. > Visit this group at http://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- 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 post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
