Discontinuous in the collective variable while using NOPBC

[mala...@gmail.com]

Dear PLUMED users,

I am performing a metadynamics simulation for 10 small molecules in water-membrane system in GROMACS 5.1.4 and PLUMED 2.3.0. My collective variables are

(1) z-component of distance between the COM of molecules and COM of all the phosphates of lipids

(2) Radius of gyration of all the 10 molecules.

The membrane is kept at the bottom of the simulation cell. During simulation the small molecules move freely in water, but are constrained to stay within the simulation cell. However, there are discontinuities in the CVs.  The jump in the CV exactly happens , when the one of the molecule attempts to cross the simulation box. Although the trajectory is continuous, and the molecules are within the applied bounds these jumps in CV (e.g 4nm to 16 nm for z-distance) continue to occur.

I have tried running plumed mentioning explicitly NOPBC for the CV, as well as with the default without NOPBC.

Help is really appreciated!

Thanks

Malay

:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::

The relevant part of my input file:

phos: GROUP NDX_FILE=PO4.ndx NDX_GROUP=PO4
c_phos: COM ATOMS=phos
smallmolecule: GROUP NDX_FILE=index.ndx NDX_GROUP=DR1f
c_smallmolecule: COM ATOMS=smallmolecule

#COLVARS
dz: DISTANCE ATOMS=c_phos,c_smallmolecule COMPONENTS NOPBC
rg: GYRATION TYPE=RADIUS ATOMS=smallmolecule
cn: COORDINATION GROUPA=smallmolecule D_0=0.0 R_0=0.3 MM=12 NN=6

# Run metadynamics Simulation

METAD ...
ARG=dz.z,rg
GRID_MIN=-20.0,0.0
GRID_MAX=40.0,28.0
GRID_SPACING=0.1,0.1
... METAD

PRINT ARG=dz.z,rg,cn,metad.bias STRIDE=1000 FILE=META

[Giovanni Bussi]

Hi.

dz is discontinuous by definition, since it can jump between +cellsize/2 and -cellsize/2. This is not a problem if:

1. Molecules never cross the boundaries (but this is not your case), or

2. You correctly define periodicity in the dz variables.

In the second case dz will behave like a TORSION that jumps from -pi to +pi.

Please read carefully the manual of DISTANCE since there is an example very similar to yours showing how to set up periodicity in this case

Giovanni

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