2013/8/22 Chandan Choudhury <[email protected]>: > > > 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. csg_stat does not include the normalization, while csg_boltzmann has an option to change that. Feel free, to send us a patch to improve the situation in csg_stat.
However for calculating the update, -k_bT*ln(dist/dist_target), it doesn't matter what the normalization of the distribution is as long as it is the same as the one of the target distribution. Due to the fact that csg_inverse uses csg_stat to calculate the distributions, it is the easiest to obtain the target distribution with csg_stat, too. Also the normalization factor won't make much difference in the overlap of the distributions as the normalization factor is always greater than 0. Christoph > > 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. -- 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.
