Hi, I am having a hard time understanding the description in the manual with regards to periodicity. Is the manual referring to PERIODIC and NOPBC as two separate things or one and the same? I am trying to explore the best set of CV for a free energy measurement between two transmembrane helices. I have defined a together-apart CV in the Y dimension, you can think of this as my main reaction coordinate, whilst the system is allowed to explore a small region of phase space in the X dimension. However, the X dimension is very restricted to prevent the absolute distance between the helices from increasing hugely beyond to where the Y CV allows (like an every growing 'hypotenuse' as the 'opposite' is unrestricted yet the 'adjacent' is). My system has a Y unit cell dimension of approx 10 ns, however, that will fluctuate due to using an NPT ensemble. Firstly, I am getting the following PLUMED warning via gromacs:
PLUMED: Action DISTANCE
PLUMED: with label d
PLUMED: between atoms 13790 13791
PLUMED: without periodic boundary conditions
PLUMED: added component to this action: d.x
PLUMED: added component to this action: d.y
PLUMED: added component to this action: d.z
PLUMED: WARNING: components will not have the proper periodicity - see manual
What periodicity? And how can I get periodicity if I define lower and upper walls? My plumed file is:
UNITS LENGTH=nm
cA: COM ATOMS=6763-6833
cB: COM ATOMS=6834-6904
#wholemolecules must always be before DISTANCE
WHOLEMOLECULES ENTITY0=6763-6833 ENTITY1=6834-6904
d: DISTANCE ATOMS=cA,cB COMPONENTS NOPBC
UPPER_WALLS ARG=d.y,d.x AT=4.5,1 KAPPA=1000.0,1000.0 EXP=2,2 EPS=2,2 OFFSET=0,0 LABEL=uwall
LOWER_WALLS ARG=d.y,d.x AT=0.0,-1 KAPPA=1000.0,1000.0 EXP=2,2 EPS=2,2 OFFSET=0,0 LABEL=lwall
metad: METAD ARG=d.y,d.x SIGMA=0.1,0.1 HEIGHT=0.3 PACE=100 GRID_SPARSE FILE=HILLS_C
PRINT ARG=d.y,d.x,metad.bias STRIDE=100 FILE=COLVAR_C
I have ignored the parameter PERIODIC in the DISTANCE parameter, as I found its description and example very confusing in a simulation which uses an NPT ensemble (and thus unit cell size would fluctuate). This was the description in the manual:
# this is a center of mass of a large group c: COM ATOMS=1-100 # this is the distance between atom 101 and the group d: DISTANCE ATOMS=c,101 COMPONENTS # this makes a new variable, dd, equal to d and periodic, with domain -10,10 # this is the right choise if e.g. the cell is orthorombic and its size in # z direction is 20. dz: COMBINE ARG=d.z PERIODIC=-10,10 # metadynamics on dd METAD ARG=dz SIGMA=0.1 HEIGHT=0.1 PACE=200
I don't quite understand how this example works, especially with a non-fixed unit cell dimension (due to changes under pressure). So I used the following example:
WHOLEMOLECULES ENTITY0=1-100 e2e: DISTANCE ATOMS=1,100 NOPBC
which was accompanied by the description:
Notice that NOPBC is used to be sure that if the end-to-end distance is larger than half the simulation box the distance is compute properly. Also notice that, since many MD codes break molecules across cell boundary, it might be necessary to use the WHOLEMOLECULESkeyword (also notice that it should be before distance).
I would like to know whether I have treated the periodic boundary condition correctly for a system in which as two molecules separate along their CVs, one of them might cross the unit cell boundary and thus appear on the opposite side? Many thanks
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