Puckering coordinates metadynamics simulations

[Felipe Nepomuceno]

HI,

I was trying to do some metadynamics simulations of the puckering of carbohydrate rings in order to observe their energy profile. I started using theta and phi as CV's, however, whenever theta approaches 0º, the variation of the phi value causes the ring to break and the simulation to stop.

Given that, I started trying to use the qx and qy as CV's and the simulation works just fine. When I open the resulting HILLS file, the values of qx and qy are stuck between 0.08 and -0.08, with a big energy minima occupying the whole graph. Right below is the .dat file I used fot the theta/phi simulation and for the qx/qy simulation:

Theta/Phi:

RESTART
PUCKERING ATOMS=14,15,7,4,1,13 LABEL=puck

UPPER_WALLS ARG=puck.theta,puck.phi AT=pi,pi KAPPA=250.0,250.0 EXP=2,2 EPS=1,1 OFFSET=0,0 LABEL=uwall
LOWER_WALLS ARG=puck.theta,puck.phi AT=0.0,0.0 KAPPA=250.0,250.0 EXP=2,2 EPS=1,1 OFFSET=0,0 LABEL=lwall
PRINT ARG=uwall.bias,lwall.bias STRIDE=500

METAD ...
LABEL=metad
ARG=puck.theta,puck.phi
PACE=500
HEIGHT=1.0
SIGMA=0.2,0.2
FILE=HILLS_theta_phi
BIASFACTOR=6.0
TEMP=298
... METAD

PRINT STRIDE=10 ARG=puck.theta,puck.phi,metad.bias FILE=COLVAR_theta_phi

ENDPLUMED

Qx/Qy:

PUCKERING ATOMS=14,15,7,4,1,13 LABEL=puck

METAD ...
LABEL=metad
ARG=puck.qx,puck.qy
PACE=500
HEIGHT=1.0
SIGMA=0.2,0.2
FILE=HILLS_qxqy
BIASFACTOR=100.0
TEMP=298
... METAD

PRINT STRIDE=10 ARG=puck.qx,puck.qy,metad.bias FILE=COLVAR_qxqy




ENDPLUMED

For both cases I used the O5-C1-C2-C3-C4-C5 order of the puckering atoms.

What am I doing wrong? Can someone think of anything that might help me elucidate the energy profile of a carbohydrate ring in function of Theta and Phi?

Thank you in advance,

Best regards,

Felipe

[Giovanni Bussi]

Hi,

for a 6 membered ring I am not sure qx and qy are sufficient. Maybe you should use qx, qy, and qz.

Giovanni

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[Vojtech Spiwok]

Hi,

Cremer-Pople coordinates are distance-unit-dependent. In a software usinig Angstroms they are (I hope) 10x higher than in software using nm.

If you expect that only one chair can occur (1C4 or 4C1) you can use qx and qy, to explore both chairs you need qz.

Vojtech Spiwok

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