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.
Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
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AB.bond.dist.tgt
Description: Binary data
AB.bond.pot.cur
Description: Binary data
AB.bond.dist.new
Description: Binary data
AB.bond.pot.new
Description: Binary data
