Hello,
I have just started using VOTCA and I am a little bit stuck with one
thing.
I have a box of dodecane chains with UA representations. I am mapping
them in groups of 3, so getting 4 beads:
C1-C2-C3-C4-C5-C6-C7-C8-C9-C10-C11-C12
-----A1---- ------B1------ -----B2----- ------A2------
So I have type A - end bead and type B center bead.
So I have 2 types of bonds AB and BB and 1 angle ABB
In the mapping.xml I name them:
<cg_bonded>
<bond>
<name>AB-bond</name>
<beads>
A1 B1
A2 B2
</beads>
<name>BB-bond</name>
<beads>
B1 B2
</beads>
</bond>
<angle>
<name>ABB-angle</name>
<beads>
A1 B1 B2
A2 B2 B1
</beads>
</angle>
</cg_bonded>
then I run the csg_boltzmann trying to get distributions and
potentials for the above. Here are my comands:
hist AB-bond.dist.ib *:AB-bond:*
hist BB-bond.dist.ib *:BB-bond:*
hist AAB-angle.dist.ib *:AAB-angle:*
tab set T 250
tab set scale bond
tab AB-bond.pot.ib *:AB-bond:*
tab BB-bond.pot.ib *:BB-bond:*
tab set scale angle
tab AAB-angle.pot.ib *:AAB-angle:*
q
For some reason in the case of AB-bonds and AAB-angles i don't get
anything:
Reading file topol.tpr, VERSION 4.5.4 (single precision)
I have 12000 beads in 1000 molecules
I have 4000 beads in 1000 molecules for the coarsegraining
Reading frames from gro file 'Generated by Ma and V amazing code : 12
system t= 0.00000', 12000 atoms.
Reading frame 0 time 0.000
Last frame 11 time 110.000
Interactive mode, expecting commands:
help: show this help
q: quit
list: list all available bonds
vals <file> <selection>: write values to file
hist <file> <selection>: create histogram
tab <file> <selection>: create tabulated potential
autocor <file> <selection>: calculate autocorrelation, only one row
allowed in selection!
cor <file> <selection>: calculate correlations, first row is
correlated with all other rows
> histogram created using 0 data-rows, written to AB-bond.dist.ib
> histogram created using 1000 data-rows, written to BB-bond.dist.ib
> histogram created using 0 data-rows, written to AAB-angle.dist.ib
> > > > histogram created using 0 data-rows, written to AB-bond.pot.ib
> histogram created using 1000 data-rows, written to BB-bond.pot.ib
> > histogram created using 0 data-rows, written to AAB-angle.pot.ib
Is there something I am not doing correctly?
Thanks
V
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