Hi Pallavi, If you keep the density (N/V) the same, different sizes of the simulation box for AA-MD and CG-MD won't make the difference. Here is why.
Assuming there are only one kind of CG particles in the system and we want to reproduce the CG-CG RDFs. Then the RDF from the MD simulation can be computed as g(r) = Npair(r) / ( dV * (N/2) *(N/V) ) where, Npair(r) is the average number of pairs at distance 'r', dV is the bin volume, N is the total number of CG particles, and V is the box volume. As you can see from above definition, as long as you keep N/V the same, difference in volumes won't matter. In other words, if you change volume "V" you should also change "N" such that N/V is set to desired density. Let us know if you have doubts about above clarification. On Wed, Dec 23, 2015 at 11:18 AM, Pallavi Banerjee < [email protected]> wrote: > Thank you for your reply, Sikandar. I am worried about the normalization > of the rdf. Isn't that a volume normalization? If that is the case, I would > think that different sizes of the simulation box for the atomistic and CG > runs would make a difference. I might be wrong here, and hence need some > clarification on this. > > Many thanks. > > -Pallavi Banerjee > > > On Wednesday, December 23, 2015 at 10:31:24 PM UTC+5:30, Pallavi Banerjee > wrote: >> >> Hello all, >> >> Should the box volume to carry out NVT runs for IBI be the very same as >> that of the atomistic run? Would the difference in volume, if there was >> any, lead to issues in the convergence of the rdf profiles? >> >> 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 https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. > -- 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 https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
