2015-10-19 12:38 GMT-06:00 Pallavi Banerjee <[email protected]>: > Yes. I could incorporate the potential of MARTINI-derived W-W interaction > directly, and leave out the iteration between W-W. But that would require me > to provide a mapping for 4 molecules of atomistic water to one bead. Can > this be possible via VOTCA? Well, VOTCA cannot make multiple molecules into one, but you can use martinize to do that: <http://www.cgmartini.nl/index.php/tools2/proteins-and-bilayers/204-martinize> that will give you the initial configuration (i.e. conf.gro, topol.top). Besides that you will need the target distributions and you can get them using gromacs analysis tools or VOTCA tools.
Christoph > > Yes, you right about the fact that both are different approaches, but since > viscosity is the protagonist here, I would begin with MARTINI and if this > doesn't work, move on to IBI for the whole system. > > Thanks! > > -Pallavi Banerjee > > > On Monday, October 19, 2015 at 11:21:13 AM UTC+5:30, Pallavi Banerjee wrote: >> >> Hello all, >> >> My system is polyacrylamide in water. I need to coarse-grain the system >> traversing through a concentration range. What I plan to do is IBI using the >> MARTINI water model since this water model gives a viscosity value close to >> that of SPC-E (water model in my atomistic system) and viscosity is the >> major property of interest in my case. IBI would then be carried out to >> optimize the potentials between the polymers and polymer-water, whereas the >> water-water interaction would be directly taken up from MARTINI. Since >> MARTINI uses a 4:1 mapping, I was wondering whether this idea would be >> viable if I am to use votca. >> >> Thanks in advance! >> >> -Pallavi Banerjee > > -- > 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.
