Hi, 2015-04-25 16:16 GMT-06:00 Vitalie Botan <[email protected]>: > Dear VOTCA users and developers, > > I have a problem in differentiating between intra- and inter-molecular > non-bonded distributions: the system under consideration consists of 3 > identical polymer chains, so normally one would need to provide a mapping > for only one of those chains and the rest is cared by VOTCA. Unfortunately > in this approach I haven't found a way to distinguish between similar beads > for inter and intra-molecular non-bonded distributions. Let's say the bead > A1 of the type A in the 1st chain is the reference bead and the bead A1 in > the 3rd chain is the observable bead. What I want to look at is the > distribution function A1_1st-A1_3rd, for example. Manipulation with the > underlying atomistic PDB file by renaming atoms or fragments from different > chains always gives mapping error when checking with csg_dump. If the naming > in original PDB is identical in all 3 chains, introducing new bead types and > names in mapping file always leads to mapping 3 different bead type into a > single chain, not different ones. > Is there a way to differentiate between different chains when calculating > non-bonded distribution functions? I think there is no easy way to achieve what you want inside VOTCA without customization. The problem basically is that VOTCA has no easy way to distinguish between different molecules of the same type. As a workaround you could create multiple mapping files and different bead types per molecule, but that will become very error-prone.
However, I would attack the problem in the following way, use the same mapping for each molecule and then write out the mapped trajectory using csg_stat. The mapped trajectory could then be analyzed by either g_dist from the gromacs package or a simple script considering on only certain beads (e.g. by filtering the atom id.) Cheers, Christoph > > Best, > > --Vitalie > > -- > 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.
