Hi, On Wed, Dec 23, 2015 at 9:26 PM, Pallavi Banerjee < [email protected]> wrote:
> Hi Sikandar, > > Thank you for your reply again. That was well explained. > > So, let's say I have only one bead type in my system. I get the target rdf > from the atomistic trajectory after having done the mapping. This would > entail that I cannot change the N (total number of beads in the system) > when running CG runs to perform IBI, since the mapping of the beads has > been already done. This would further mean that I cannot change the volume > of the system because I need to have N/V the same in both atomistic and CG > systems for the rdfs to make sense. Am I right here? > Yes, you are right. If you are creating the CG system by mapping the AA system, then to keep the density same, you should not change the volume of the CG system. However, if you still want to change the box volume, you can do so while keeping the density the same. Here is how. I am assuming you are using GROMACS MD engine. In that case, with the help of "gmx solvate" tool, you can use the mapped CG system obtained from the AA trajectory as a reference solvent box to create CG system of desired volume and density. For example, let's say you mapped one frame from AA trajectory and saved it as "CG.gro", then you can create CG configuration of desired volume V and N particles, where N/V is the density of reference AA system, as gmx solvate -cs CG.gro -o CG_V.gro -box Lx Ly Lz -maxsol N where, Lx = Ly = Lz = V^(1/3). I hope it clarifies. Best, Sikandar > > Apologies if this is too inane a discussion. > > 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.
