Hi all,
I am facing a problem with using RMSD. So basically the way RMSD in plumed works is
RMSD REFERENCE=file.pdb TYPE=OPTIMAL
where the RMSD is computed by aligning the atoms mentioned in file.pdb and the instantaneous position of those atoms.
However, I am particularly interested in computing and biasing the RMSD for two sub domains of my system. So what I require is I align the structure for all but the two sub domains containing a certain range of residues of my protein system and then compute the RMSD for the two sub domains.
But the way plumed does is it asks for reference file in which
either
I could include only those sub domain residues and compute their RMSD but the issue is that these residues would be aligned and hence RMSD would be affected.
or
I could include all but those sub domain residues so that they get aligned and not sub domain residues, but in this case the RMSD won't be computed for the sub domain residues.
Can anyone please suggest a workaround ? Please let me know if further explanation is required to understand the issue. Thank You.
I am attaching my plumed script: The RMSD of the sub domains residues is what I am using as my CV.
-Keshav Patil
University of Pennsylvania
UNITS LENGTH=A ENERGY=kcal/mol
MOLINFO STRUCTURE=egfr_active.pdb
WHOLEMOLECULES RESIDUES=all MOLTYPE=protein
#RMSD to inactive structure alpha C helix
RMSD REFERENCE=egfr_inactive_CA_alphaChelix.pdb TYPE=OPTIMAL LABEL=inactive_rmsd_alphaChelix
#RMSD to active structure alpha C helix
RMSD REFERENCE=egfr_active_CA_alphaChelix.pdb TYPE=OPTIMAL LABEL=active_rmsd_alphaChelix
#RMSD to inactive structure activation loop
RMSD REFERENCE=egfr_inactive_CA_aloop.pdb TYPE=OPTIMAL LABEL=inactive_rmsd_aloop
#RMSD to active structure activation loop
RMSD REFERENCE=egfr_active_CA_aloop.pdb TYPE=OPTIMAL LABEL=active_rmsd_aloop
METAD ...
ARG=active_rmsd_alphaChelix,active_rmsd_aloop
SIGMA=0.05,0.05
HEIGHT=0.6
PACE=500
LABEL=meta
TEMP=300
BIASFACTOR=30
GRID_MIN=-1,-1
GRID_MAX=10,18
WALKERS_N=4
WALKERS_ID=0
WALKERS_DIR=../
WALKERS_RSTRIDE=500
... METAD
FLUSH STRIDE=500
ENERGY LABEL=energy
PRINT ARG=* STRIDE=500 FILE=COLVARS
