ALPHARMSD for four chains

[azade...@gmail.com]

Dear all,

I have four chains in my system. As a reference structure I give a PDB file in which the four chains are distinguishable with different chain names and I select each chain using the selection syntax of MDAnalysis. However, when I define the ALPHARMSD collective variable using all residues, it prints the value only for one chain. 

However,  when I give a PDB file, in which the chains are not defined, a correct number is printed to the colvar file.

Here is the colvar file:

MOLINFO STRUCTURE=protein.pdb MOLTYPE=protein PYTHON_BIN=python
WHOLEMOLECULES ENTITY0=1-4336
 
cv1: RMSD REFERENCE=protein_backbone.pdb NOPBC TYPE=OPTIMAL
cv2: ALPHARMSD RESIDUES=all NOPBC 

com1: COM ATOMS={@mda:{protein and backbone and segid PROA}}
com2: COM ATOMS={@mda:{protein and backbone and segid PROB}}
com3: COM ATOMS={@mda:{protein and backbone and segid PROC}}
com4: COM ATOMS={@mda:{protein and backbone and segid PROD}}

com: CENTER ATOMS=com1,com2,com3,com4

d1: DISTANCE ATOMS=com,com1
d2: DISTANCE ATOMS=com,com2
d3: DISTANCE ATOMS=com,com3
d4: DISTANCE ATOMS=com,com4

PRINT ARG=cv1,cv2,d1,d2,d3,d4 FILE=COLVAR STRIDE=200

I would be thankful if you could help me to solve this problem.

Best,

Azadeh

[azade...@gmail.com]

It seems the problem is that plumed considers unique resids and not all the residues with the same resids. In my systems the four chains have the same resid range.