[votca] csg_boltzmann distribution

Chandan Choudhury Mon, 30 Dec 2013 07:58:15 -0800

Dear votca users,

I am iterating the bonded part of the polymer (with following sequence:
A1-B1-C1-B2-D1-B3-C2-B4-D2-B5-C3-E1).


I am generating bond distribution using the csg_boltzmann utility.
The mapping file contains the bonds, angles and dihedrals information.

When I try to generate the bond distributions for the beads consisting of
additional bonds (1-4) and angles. The distributions obtained doesnot
matches with the one generated by not including the extra bonds & angles.

I have attached both the mapping files. map.xml consists the information
about the additions bonds & angle while map1.xml do not contain these.

*command used:*
cat csg_boltzmann.txt | csg_boltzmann  --trj 70-91_PC-trimer_whole.xtc
--top mdtrim510K_41-91ns.tpr  --cg map1.xml

&
cat csg_boltzmann.txt | csg_boltzmann  --trj 70-91_PC-trimer_whole.xtc
--top mdtrim510K_41-91ns.tpr  --cg map.xml

The BD_map.bond and BC_map.bond are obtained using the map.xml (containing
the additional bond information) file.

This behavior is only shown for BC & BD beads. For my case I donot see any
significant effect in the angle distributions.
The BC.bond and BD.bond matches with the distributions generated from
myself.

Why is this happening? What am I missing? Any guidance would be very
helpful.

Chandan


--
Chandan kumar Choudhury
NCL, Pune
INDIA

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hist AB.bond *AB.bond*
hist BC.bond *BC.bond*
hist BD.bond *BD.bond*
hist CE.bond *CE.bond*
hist A1B2.bond *A1B2.bond*
hist B1D1.bond *B1D1.bond*
hist C1B3.bond *C1B3.bond*
hist D2E1.bond *D2E1.bond*
hist ABC.angle *ABC.angle*
hist BCB.angle *BCB.angle*
hist CBD.angle *CBD.angle*
hist BDB.angle *BDB.angle*
hist BCE.angle *BCE.angle*
hist ABB.angle *ABB.angle*
hist ACB.angle *ACB.angle*
hist BCD.angle *BCD.angle*
hist BBD.angle *BBD.angle*
hist CBB.angle *CBB.angle*
hist CDB.angle *CDB.angle*
hist DBE.angle *DBE.angle*
hist DCE.angle *DCE.angle*
hist ABCB.dihedral *ABCB.dihedral*
hist BCBD.dihedral *BCBD.dihedral*
hist CBDB.dihedral *CBDB.dihedral*
hist DBCE.dihedral *DBCE.dihedral*
tab set scale dihedral
tab ABCB.dihedral.pot *ABCB.dihedral*
tab BCBD.dihedral.pot *BCBD.dihedral*
tab CBDB.dihedral.pot *CBDB.dihedral*
tab DBCE.dihedral.pot *DBCE.dihedral*
tab set T 480
tab set scale bond
tab AB.bond.pot *AB.bond*
tab BC.bond.pot *BC.bond*
tab BD.bond.pot *BD.bond*
tab CE.bond.pot *CE.bond*
tab A1B2.bond.pot *A1B2.bond*
tab B1D1.bond.pot *B1D1.bond*
tab C1B3.bond.pot *C1B3.bond*
tab D2E1.bond.pot *D2E1.bond*
tab set T 480
tab set scale angle
tab ABC.angle.pot *ABC.angle*
tab BCB.angle.pot *BCB.angle*
tab CBD.angle.pot *CBD.angle*
tab BDB.angle.pot *BDB.angle*
tab BCE.angle.pot *BCE.angle*
tab ABB.angle.pot *ABB.angle*
tab ACB.angle.pot *ACB.angle*
tab BCD.angle.pot *BCD.angle*
tab BBD.angle.pot *BBD.angle*
tab CBB.angle.pot *CBB.angle*
tab CDB.angle.pot *CDB.angle*
tab DBE.angle.pot *DBE.angle*
tab DCE.angle.pot *DCE.angle*
q

<cg_molecule>
	<name>POLCAR</name>
	<ident>tricarb</ident>
	<topology>
		<cg_beads>
			<cg_bead>
				<name>A1</name>
				<type>A</type>
				<mapping>A</mapping>
				<beads>1:mma:CT1 1:mma:HC1 1:mma:CT2 1:mma:HC2 1:mma:HC3 1:mma:HC4 1:mma:CT3 1:mma:HC7 1:mma:HC6 1:mma:HC5 </beads>
			</cg_bead>
			<cg_bead>
				<name>B1</name>
				<type>B</type>
				<mapping>B</mapping>
				<beads>1:mma:CB1 1:mma:CB5 1:mma:CB2 1:mma:CB4 1:mma:H9  1:mma:CB3 1:mma:H6  1:mma:CB6 1:mma:H8  1:mma:H7  </beads>
			</cg_bead>
			<cg_bead>
				<name>C1</name>
				<type>C</type>
				<mapping>C</mapping>
				<beads>1:mma:O1  1:mma:C   1:mma:OS  1:mma:O2  </beads>
			</cg_bead>
			<cg_bead>
				<name>B2</name>
				<type>B</type>
				<mapping>B</mapping>
				<beads>1:mma:CA4 1:mma:CA5 1:mma:H4  1:mma:CA3 1:mma:H5  1:mma:CA6 1:mma:H3  1:mma:CA2 1:mma:H1  1:mma:CA1 </beads>
			</cg_bead>
			<cg_bead>
				<name>D1</name>
				<type>D</type>
				<mapping>D</mapping>
				<beads>2:mmb:CT1 2:mmb:CT2 2:mmb:HC2 2:mmb:HC3 2:mmb:HC4 2:mmb:CT3 2:mmb:HC7 2:mmb:HC6 2:mmb:HC5 </beads>
			</cg_bead>
			<cg_bead>
				<name>B3</name>
				<type>B</type>
				<mapping>B</mapping>
				<beads>2:mmb:CB1 2:mmb:CB5 2:mmb:CB2 2:mmb:CB4 2:mmb:H9  2:mmb:CB3 2:mmb:H6  2:mmb:CB6 2:mmb:H8  2:mmb:H7  </beads>
			</cg_bead>
			<cg_bead>
				<name>C2</name>
				<type>C</type>
				<mapping>C</mapping>
				<beads>2:mmb:O1  2:mmb:C   2:mmb:OS  2:mmb:O2  </beads>
			</cg_bead>
			<cg_bead>
				<name>B4</name>
				<type>B</type>
				<mapping>B</mapping>
				<beads>2:mmb:CA4 2:mmb:CA5 2:mmb:H4  2:mmb:CA3 2:mmb:H5  2:mmb:CA6 2:mmb:H3  2:mmb:CA2 2:mmb:H1  2:mmb:CA1 </beads>
			</cg_bead>
			<cg_bead>
				<name>D2</name>
				<type>D</type>
				<mapping>D</mapping>
				<beads>3:mmc:CT1 3:mmc:CT2 3:mmc:HC2 3:mmc:HC3 3:mmc:HC4 3:mmc:CT3 3:mmc:HC7 3:mmc:HC6 3:mmc:HC5 </beads>
			</cg_bead>
			<cg_bead>
				<name>B5</name>
				<type>B</type>
				<mapping>B</mapping>
				<beads>3:mmc:CB1 3:mmc:CB5 3:mmc:CB2 3:mmc:CB4 3:mmc:H9  3:mmc:CB3 3:mmc:H6  3:mmc:CB6 3:mmc:H8  3:mmc:H7  </beads>
			</cg_bead>
			<cg_bead>
				<name>C3</name>
				<type>C</type>
				<mapping>C</mapping>
				<beads>3:mmc:O1  3:mmc:C   3:mmc:OS  3:mmc:O2  </beads>
			</cg_bead>
			<cg_bead>
				<name>E1</name>
				<type>E</type>
				<mapping>E</mapping>
				<beads>3:mmc:CA4 3:mmc:CA5 3:mmc:H4  3:mmc:CA3 3:mmc:H5  3:mmc:CA6 3:mmc:H3  3:mmc:CA2 3:mmc:H1  3:mmc:CA1 3:mmc:H2  </beads>
			</cg_bead>
		</cg_beads>
		<cg_bonded>
			<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>
			<bond>
				<name>A1B2.bond</name>
				<beads>
				A1 B2
				</beads>
			</bond>
			<bond>
				<name>B1D1.bond</name>
				<beads>
				B1 D1
				D1 B4
				B3 D2
				</beads>
			</bond>
			<bond>
				<name>C1B3.bond</name>
				<beads>
				C1 B3
				B2 C2
				C2 B5
				B4 C3
				</beads>
			</bond>
			<bond>
				<name>D2E1.bond</name>
				<beads>
				D2 E1
				</beads>
			</bond>
			<angle>
				<name>ABC.angle</name>
				<beads>
				A1 B1 C1
				</beads>
			</angle>
			<angle>
				<name>BCB.angle</name>
				<beads>
				B1 C1 B2
				B3 C2 B4
				</beads>
			</angle>
			<angle>
				<name>CBD.angle</name>
				<beads>
				C1 B2 D1
				D1 B3 C2
				C2 B4 D2
				D2 B5 C3
				</beads>
			</angle>
			<angle>
				<name>BDB.angle</name>
				<beads>
				B2 D1 B3
				B4 D2 B5
				</beads>
			</angle>
			<angle>
				<name>BCE.angle</name>
				<beads>
				B5 C3 E1
				</beads>
			</angle>
			<angle>
				<name>ABB.angle</name>
				<beads>
				A1 B1 B2
				</beads>
			</angle>
			<angle>
				<name>ACB.angle</name>
				<beads>
				A1 C1 B2
				</beads>
			</angle>
			<angle>
				<name>BCD.angle</name>
				<beads>
				B1 C1 D1
				B3 C2 D2
				D1 C2 B4
				</beads>
			</angle>
			<angle>
				<name>BBD.angle</name>
				<beads>
				B1 B2 D1
				B3 B4 D2
				D1 B3 B4
				</beads>
			</angle>
			<angle>
				<name>CBB.angle</name>
				<beads>
				C1 B2 B3
				C2 B4 B5
				B2 B3 C2
				B4 B5 C3
				</beads>
			</angle>
			<angle>
				<name>CDB.angle</name>
				<beads>
				C1 D1 B3
				C2 D2 B5
				B2 D1 C2
				B4 D2 C3
				</beads>
			</angle>
			<angle>
				<name>DBE.angle</name>
				<beads>
				D2 B5 E1
				</beads>
			</angle>
			<angle>
				<name>DCE.angle</name>
				<beads>
				D2 C3 E1
				</beads>
			</angle>
			<dihedral>
				<name>ABCB.dihedral</name>
				<beads>
				A1 B1 C1 B2
				</beads>
			</dihedral>
			<dihedral>
				<name>BCBD.dihedral</name>
				<beads>
				B1 C1 B2 D1
				D1 B3 C2 B4
				B3 C2 B4 D2
				</beads>
			</dihedral>
			<dihedral>
				<name>CBDB.dihedral</name>
				<beads>
				C1 B2 D1 B3
				B2 D1 B3 C2
				C2 B4 D2 B5
				B4 D2 B5 C3
				</beads>
			</dihedral>
			<dihedral>
				<name>DBCE.dihedral</name>
				<beads>
				D2 B5 C3 E1
				</beads>
			</dihedral>
		</cg_bonded>
	</topology>
	<maps>
		<map>
			<name>A</name>
			<weights>12 1 12 1 1 1 12 1 1 1</weights>
		</map>
		<map>
			<name>B</name>
			<weights>12 12 12 12  1 12 1 12 1 1</weights>
		</map>
		<map>
			<name>C</name>
			<weights>16 12 16 16</weights>
		</map>
		<map>
			<name>D</name>
			<weights>12 12 1 1 1 12 1 1 1</weights>
		</map>
		<map>
			<name>E</name>
			<weights>12  12  1  12  1  12  1  12  1  12  1</weights>
		</map>
	</maps>
</cg_molecule>

<cg_molecule>
	<name>POLCAR</name>
	<ident>tricarb</ident>
	<topology>
		<cg_beads>
			<cg_bead>
				<name>A1</name>
				<type>A</type>
				<mapping>A</mapping>
				<beads>1:mma:CT1 1:mma:HC1 1:mma:CT2 1:mma:HC2 1:mma:HC3 1:mma:HC4 1:mma:CT3 1:mma:HC7 1:mma:HC6 1:mma:HC5 </beads>
			</cg_bead>
			<cg_bead>
				<name>B1</name>
				<type>B</type>
				<mapping>B</mapping>
				<beads>1:mma:CB1 1:mma:CB5 1:mma:CB2 1:mma:CB4 1:mma:H9  1:mma:CB3 1:mma:H6  1:mma:CB6 1:mma:H8  1:mma:H7  </beads>
			</cg_bead>
			<cg_bead>
				<name>C1</name>
				<type>C</type>
				<mapping>C</mapping>
				<beads>1:mma:O1  1:mma:C   1:mma:OS  1:mma:O2  </beads>
			</cg_bead>
			<cg_bead>
				<name>B2</name>
				<type>B</type>
				<mapping>B</mapping>
				<beads>1:mma:CA4 1:mma:CA5 1:mma:CA1 1:mma:CA3 1:mma:H5  1:mma:CA6 1:mma:H3  1:mma:CA2 1:mma:H1  1:mma:H4 </beads>
			</cg_bead>
			<cg_bead>
				<name>D1</name>
				<type>D</type>
				<mapping>D</mapping>
				<beads>2:mmb:CT1 2:mmb:CT2 2:mmb:HC2 2:mmb:HC3 2:mmb:HC4 2:mmb:CT3 2:mmb:HC7 2:mmb:HC6 2:mmb:HC5 </beads>
			</cg_bead>
			<cg_bead>
				<name>B3</name>
				<type>B</type>
				<mapping>B</mapping>
				<beads>2:mmb:CB1 2:mmb:CB5 2:mmb:CB2 2:mmb:CB4 2:mmb:H9  2:mmb:CB3 2:mmb:H6  2:mmb:CB6 2:mmb:H8  2:mmb:H7  </beads>
			</cg_bead>
			<cg_bead>
				<name>C2</name>
				<type>C</type>
				<mapping>C</mapping>
				<beads>2:mmb:O1  2:mmb:C   2:mmb:OS  2:mmb:O2  </beads>
			</cg_bead>
			<cg_bead>
				<name>B4</name>
				<type>B</type>
				<mapping>B</mapping>
				<beads>2:mmb:CA4 2:mmb:CA5 2:mmb:CA1 2:mmb:CA3 2:mmb:H5  2:mmb:CA6 2:mmb:H3  2:mmb:CA2 2:mmb:H1  2:mmb:H4  </beads>
			</cg_bead>
			<cg_bead>
				<name>D2</name>
				<type>D</type>
				<mapping>D</mapping>
				<beads>3:mmc:CT1 3:mmc:CT2 3:mmc:HC2 3:mmc:HC3 3:mmc:HC4 3:mmc:CT3 3:mmc:HC7 3:mmc:HC6 3:mmc:HC5 </beads>
			</cg_bead>
			<cg_bead>
				<name>B5</name>
				<type>B</type>
				<mapping>B</mapping>
				<beads>3:mmc:CB1 3:mmc:CB5 3:mmc:CB2 3:mmc:CB4 3:mmc:H9  3:mmc:CB3 3:mmc:H6  3:mmc:CB6 3:mmc:H8  3:mmc:H7  </beads>
			</cg_bead>
			<cg_bead>
				<name>C3</name>
				<type>C</type>
				<mapping>C</mapping>
				<beads>3:mmc:O1  3:mmc:C   3:mmc:OS  3:mmc:O2  </beads>
			</cg_bead>
			<cg_bead>
				<name>E1</name>
				<type>E</type>
				<mapping>E</mapping>
				<beads>3:mmc:CA4 3:mmc:CA5 3:mmc:H4  3:mmc:CA3 3:mmc:H5  3:mmc:CA6 3:mmc:H3  3:mmc:CA2 3:mmc:H1  3:mmc:CA1 3:mmc:H2  </beads>
			</cg_bead>
		</cg_beads>
		<cg_bonded>
			<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>
			<angle>
				<name>ABC.angle</name>
				<beads>
				A1 B1 C1
				</beads>
			</angle>
			<angle>
				<name>BCB.angle</name>
				<beads>
				B1 C1 B2
				B3 C2 B4
				</beads>
			</angle>
			<angle>
				<name>CBD.angle</name>
				<beads>
				C1 B2 D1
				D1 B3 C2
				C2 B4 D2
				D2 B5 C3
				</beads>
			</angle>
			<angle>
				<name>BDB.angle</name>
				<beads>
				B2 D1 B3
				B4 D2 B5
				</beads>
			</angle>
			<angle>
				<name>BCE.angle</name>
				<beads>
				B5 C3 E1
				</beads>
			</angle>
            <dihedral>
                <name>ABCB.dihedral</name>
                <beads>
                A1 B1 C1 B2
                </beads>
            </dihedral>
            <dihedral>
                <name>BCBD.dihedral</name>
                <beads>
                B1 C1 B2 D1
                D1 B3 C2 B4
                B3 C2 B4 D2
                </beads>
            </dihedral>
            <dihedral>
                <name>CBDB.dihedral</name>
                <beads>
                C1 B2 D1 B3
                B2 D1 B3 C2
                C2 B4 D2 B5
                B4 D2 B5 C3
                </beads>
            </dihedral>
            <dihedral>
                <name>DBCE.dihedral</name>
                <beads>
                D2 B5 C3 E1
                </beads>
            </dihedral>
		</cg_bonded>
	</topology>
	<maps>
		<map>
			<name>A</name>
			<weights>12 1 12 1 1 1 12 1 1 1</weights>
		</map>
		<map>
			<name>B</name>
			<weights>12 12 12 12  1 12 1 12 1 1</weights>
		</map>
		<map>
			<name>C</name>
			<weights>16 12 16 16</weights>
		</map>
		<map>
			<name>D</name>
			<weights>12 12 1 1 1 12 1 1 1</weights>
		</map>
		<map>
			<name>E</name>
			<weights>12  12  1  12  1  12  1  12  1  12  1</weights>
		</map>
	</maps>
</cg_molecule>

BD.bond
Description: Binary data

BD_map.bond
Description: Binary data

BC.bond
Description: Binary data

BC_map.bond
Description: Binary data

[votca] csg_boltzmann distribution

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