RMSD and PBC

[arbeitskr...@gmail.com]

Dear,
I'm using the RMSD as a colvar in a WTmetadynamics simulation of a protein and am seeing discontinuities in the RMSD value, even though i'm using the WHOLEMOLECULES directive. I'm using gromacs 4.6.3 with Plumed 2.0.0. Below are my plumed input file and the first lines of the refence pdb. Except for the discontinuities, the RMSD is the same as I obtain with for example the gromacs tools. When looking at the trajectory the discontinuities do not (always) coincide with the protein moving over the box boundary.

What am I doing wrong? Could the tilted box be the problem?
Thanks,
Djurre


WHOLEMOLECULES ENTITY0=1-326
RMSD REFERENCE=ref-BB.pdb TYPE=OPTIMAL LABEL=rmsd
METAD ...
ARG=rmsd SIGMA=.01 HEIGHT=0.1 PACE=100 LABEL=restraint BIASFACTOR=2 TEMP=293
... METAD
PRINT ARG=rmsd.* FILE=rmsd.dat STRIDE=1000
PRINT ARG=restraint.* FILE=restraint.dat STRIDE=1000


TITLE     2 INTERACTION
REMARK    THIS IS A SIMULATION BOX
CRYST1  121.951  121.951  121.951  60.00  60.00  90.00 P 1           1
MODEL        1
ATOM      1  BB  MET A   1      87.941 112.804  52.137  1.00  1.00           B
ATOM      3  BB  GLN A   2      88.893 109.579  53.879  1.00  1.00           B
ATOM      5  BB  ILE A   3      88.934 106.210  52.157  1.00  1.00           B



 

[Giovanni Bussi]

Hi!

"Except for the discontinuities": I assume plumed file is continuous and gromacs one has jumps. This is expected, it is an effect of WHOLEMOLECULES. You can check if everything is correct doing:

DUMPATOMS ATOMS=1-326 FILE=tests.gro

after the WHOLEMOLECULES command. This will produce a gro file with whole molecules. If you use gromacs tools on that the result should be identical to the one given by PLUMED.

Notice that if the whole molecule jumps across PBC there is no problem. The problem is when the molecule is broken (half in one part of the box, half in another part).

Ciao!

Giovanni

 

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