2013/3/25 Mercadante, Davide <davide.mercada...@h-its.org> > > Dear Christoph, > > I am writing because I have a question about preparing my system for CG > simulations using votca. Welcome, and please if your research is not top-secret, post your questions on our mailing list: <votca@googlegroups.com>, so that others can learn from it. > > I want to simulate a peptide in water using a CG approach and I was thinking > of using votca to determine the non-bonded and bonded CG potentials starting > from the full atom simulations that I have already performed on the same > system (using Gromacs ersion 4.5.5). In order to do this I have studied the > votca manual and I found it very interesting. I am interested to apply > Boltzmann inversion method to find out bonded potential and IBI to determine > the bonded potential in order to build a gromacs topology to use in further > simulations. > > However, I have a question about calculating the non-bonded potential. It > seems to me that I have to "feed" votca with a settings.xml file that lists > all the non-bonded interactions occurring and other parameters to carry out > IBI. However, in my system (not very small) the list of non-bonded > interactions will be possibly very long..there is an automated way to build > the settings file? How I can get a list of non-bonded interactions in my > system?
I am sorry to tell you that there is no automated way to create these xml files, we thought about that several times, but as it can be done with a 10 line shell script and most interactions will have different ranges, which will need some tweaking anyhow, we never wrote a program to do it. I can post my script if you need it! Cheers, Christoph > > Thank you in advance for your time and please accept my apologies if this is > a stupid question. I am a newbie of votca. > > Cheers, > Davide > > ********************************************** > Davide Mercadante Ph.D. > Postdoctoral Fellow > Heidelberg Institute for Theoretical Studies – HITS > Schloss-Wolfsbrunnenweg, 35 > D-69118 Heidelberg, Germany. > ********************************************** > > -- > 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 votca+unsubscr...@googlegroups.com. To post to this group, send email to votca@googlegroups.com. Visit this group at http://groups.google.com/group/votca?hl=en. For more options, visit https://groups.google.com/groups/opt_out.
