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. 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. 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.
