On Tuesday, 21 January 2014 17:24:36 UTC+1, Christoph Junghans wrote: > > 2014/1/21 Jakub Krajniak <[email protected] <javascript:>>: > > Hi all, > > > > I am playing with Votca from a couple of weeks to get the effective > > potential of quite simple polymer system. > > Mainly I have very short (4 beads) polymer that I want to coarse grained > to > > two beads. In total there > > are 100 of 'chains' in the box. In the fine scale there are angle, bond > and > > dihedral potentials to define the structure > > of those 'chains'. The fine-scale simulation are governed by the > espressopp > > that gave me the trajectory file. The > > bond distribution, angles, dihedrals, fluctuations of temperature and > total > > energy seems fine so I assumed that > > the fine-scale simulation is correct. > > > > On the CG level I have actually only the bond potential and the > > intermolecular potential. That simulation is also running on the > espressopp. > > For the bond potential I have used the csg_boltzmann to get it. And here > > comes the first question: > > 1. What temperature should be set in the csg_boltzmann? For the > fine-scale > > simulation I am using temperature defined by (T/kB<epsilon>) and my > kB=1.0; > > Also what temperature should be set in the <kBT> tag for the <inverse>? > csg_boltzmann has gromacs units hard-coded. > > I would suggest to write out the potentials with standard > normalization (no bond/angle correction) and to use awk (see previous > post on the mailing list) or > csg_inverse's script to create an initial potential: > $ csg_call --options settings.xml --ia-name bond --ia-type bond > prepare_single ibi > (only available in VOTCA 1.3)
Thank you very much for the bunch of advices! It seems that the issue was related to this part, I had a wrong bond potential. Best regards, Jakub Krajniak -- 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/groups/opt_out.
