problem met with RMSD calculation with WHOLEMOLECULES

[Luke Lin]

Hi all,

I am using PLUMED 2.3.4 to calculate RMSD together with WHOLEMOLECULES. I am testing a case where there is a broken molecule. The result seems to be different from if I correct the broken molecule by Gromacs itself. I am wondering what would be the source of this problem.

I attached the tmp.protein.gro, which is a broken molecule by PBC condition. Another one, tmp.protein.pbccorrected.gro is the PBC corrected structure using Gromacs command "trjconv". processed.native.pdb is the native state PDB, and newbox.pdb is a PDB file specifying the box used in my simulation (I am not sure if I can just use processed.native.pdb in MOLINFO). My plumed file is like:

MOLINFO STRUCTURE=newbox.pdb

WHOLEMOLECULES RESIDUES=all MOLTYPE=protein

RMSD ...

REFERENCE=processed.native.pdb

TYPE=OPTIMAL

LABEL=rmsd

... RMSD

PRINT ARG=rmsd.* FILE=rmsd.txt

plumed driver --plumed plumed.dat --igro tmp.protein.pbccorrected.gro

gives me

 0.000000 0.519645

While

plumed driver --plumed plumed.dat --igro tmp.protein.gro

gives:

0.000000 1.072241

I am not sure what can be the source of this problem. Could anyone help me out?

Thanks,

Luke

[Giovanni Bussi]

Hi,

I think that RESIDUES=all only selects backbone atoms. Please check with DUMPATOMS which atoms are made whole. You might have to specify explicitly a list with WHOLEMOLECULES ENTITY0=...

Giovanni

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[arbeitskr...@gmail.com]

Hi Luke,

I had some issues with calculating the RMSD with plumed when using a reference structure from a simulation with a cubic box for RMSD calculation in a simulation with a truncated octahedron. Im not completely sure whats the reason for this, but switching to a cubic box in my simulations fixed the problem. (I calculated the RMSD of a ligand in a protein/ligand complex on the fly. The reference structure was taken from a long equilibrium simulation in a truncated octahedron. The simulation itself was then in a cubic box.)

Greets,
Alex

[Luke Lin]

Hi Giovanni,

Thanks and it is indeed what you suggested, I checked the DUMPATOMS and find the RESIDUES=all only correct the backbone atoms, without doing anything for the sidechains. After using ENTITY0, it solves my problem!

Thanks again,

Luke

[Luke Lin]

Hi Alex,

I don't think you can use a different PBC box in between doing simulation and doing the calculations of RMSD. It is better to keep the consistency throughout.

Best,

Luke