Hey Denis thanks very much for the explanation. I will read the papers you referred to for more understanding.
On different issue, which may not be directly related to this group, can anyone here advice me on how to compute two-body PMF, which IBI reproduces, from all atom MD trajectory data. I mean, method other than using Boltzman law and g(r) infromation. thanks sikandar On Thu, Oct 7, 2010 at 3:15 PM, Denis Andrienko <[email protected]>wrote: > Dear Sikandar, > > FM is trying to reproduce many-body PMF. IBI reproduces two-body PMF. > In principle, if you have large enough basis set for FM, it should > eventually give you the two-body PMF. However, two-body potentials > (sometimes three- and four-body) which are normally used to describe > interactions between CG beads often do not form a complete basis set > (e.g. water) and hence FM potentials do not reproduce two-body PMF. > > You can read more in these papers: > > http://m.jcp.aip.org/resource/1/jcpsa6/v128/i24/p244114_s1 > http://pubs.acs.org/doi/abs/10.1021/ct900369w > > cheers, > Denis > > On Oct 7, 9:06 pm, Sikandar Mashayak <[email protected]> wrote: > > Hi > > > > As per my understanding, IBI tries to equate PMF profile in all atom and > CG > > representation of system. In Force-Matching technique, CG potential is > > parameterized such that forces on CG site are reproduced, does that mean > PMF > > is also matched? And if so, IBI CG and FM CG potential should be the > same, > > right? > > > > thanks > > sikandar > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected] <votca%[email protected]>. > For more options, visit this group at > http://groups.google.com/group/votca?hl=en. > > -- You received this message because you are subscribed to the Google Groups "votca" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/votca?hl=en.
