On Thu, Aug 22, 2013 at 8:46 PM, Christoph Junghans <[email protected]>wrote:
> 2013/8/22 Chandan Choudhury <[email protected]>: > > Dear votca users, > > > > I am stucked in some basic work flow of CG. > > > > I am using 1.3-dev version of votca with gmx 4.6.3. > > > > I have generated the distributions of bonds of the beads from the mapped > > atomistic simulation. The beads are in the following sequence > > A1-B1-C1-B2-D1-B3-C2-B4-D2-B5-C3-E1. Bonds are defined in the cg mapping > > file as: > > <bond> <name>AB.bond</name> <beads> > > A1 B1 > > </beads> </bond> > > <bond> <name>BC.bond</name> <beads> > > B1 C1 > > C1 B2 > > B3 C2 > > C2 B4 > > B5 C3 > > </beads> </bond> > > <bond> <name>BD.bond</name> <beads> > > B2 D1 > > D1 B3 > > B4 D2 > > D2 B5 > > </beads> </bond> > > <bond> <name>CE.bond</name> <beads> > > C3 E1 > > </beads> </bond> > > > > First, I have computed all the bonded distributions and then normalized > it > > and inverted to obtain the respective potentials. I have also calculated > the > > force (-dV/dr). This potential and force severs as an input for the > > step_001. I have attached the distribution and potential (for AB bead). > > After the completion of step_001, I obtain the distributions and > potentials > > (*.new). I see that in step_001 the AB.bond samples different space (fig > > attached). As the sampling regions are not overlapping, so the potential > > update would be wrong. The same behaviour is also observed for the > BD.bond. > > While BC and CE bonds shows resonable distributions. Can someone guide > me > > regarding this? The potential for the AB.bond dips around 0.34. So, the > > same should also be reflected in the AB.bond distribution. Hope I am > making > > a correct statement. What would be the possible reasons that forces the > AB > > bond to sample around 0.37 instead for 0.34 nm? Any insight would be very > > helpful. > > It looks like something might be wrong in your coarse-grained topology. I will have a re-look at the topology. > > It could also be problematic to iterate on all interactions at the > same time. Play with do_potential in your settings file. > You could also try to coarse grain the bonded interactions first from > a single molecule in vacuum. > Or replace the bonded interactions by a very stiff springs and iterate > on the non-bonded interactions first and then do IBI on the springs > again. > > Btw, the target distributions for csg_inverse for bonded interactions > should be calculated with csg_stat and hence don't include the 1/r^2 > and 1/sin normalization. > Does it imply that csg_stat includes the normalization. As the distributions overlap with the csg_boltzmann output, then it should also include the normalization. Chandan > > Christoph > > > > > > Chandan > > > > -- > > Chandan kumar Choudhury > > NCL, Pune > > INDIA > > > > -- > > 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/groups/opt_out. > > > > -- > 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/groups/opt_out. > -- 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/groups/opt_out.
