HOW to set INTERVAL in plumed 2.0.2

[xianqiang sun]

Dear all,

I am using the plumed 2.0.2 with a distance and a dihedral as the collective variables for adding biased potentials.

I tried to find an example on setting the the lower and upper limits for adding biased potentials for the distance with the keyword INTERVAL. But I did not find one.

Here I post my input files which is not working because the biased potential is still added in the output HILLS file when the distance is smaller than -0.5nm.

COM ATOMS=1-24 LABEL=com1

DISTANCE ATOMS=2832,com1 LABEL=d1 COMPONENTS

TORSION ATOMS=3571,3573,3575,3578 LABEL=a1

COMBINE ARG=d1.z PERIODIC=-9.68850,9.68850 LABEL=dz

UPPER_WALLS ARG=dz AT=4.5 KAPPA=150.0 EXP=2 EPS=1 OFFSET=0 LABEL=uwall

LOWER_WALLS ARG=dz AT=-0.3 KAPPA=150.0 EXP=2 EPS=1 OFFSET=0 LABEL=lwall

METAD ARG=dz,a1 INTERVAL=dz SIGMA=0.05 HEIGHT=0.3 BIASFACTOR=12 TEMP=300 PACE=250 LABEL=restraint ADAPTIVE=GEOM

PRINT ARG=dz,a1,restraint.bias,uwall.bias FILE=colvar STRIDE=200

ENDPLUMED

Thanks so much for your kind help in resolving my problem.

Best regards,

[cecil...@gmail.com]

Hello,

I have exactly the same question. Did you manage to find how to use the keyword INTERVAL?


Best regards,

[Muneeb Sultan]

It says on the website 

https://plumed.github.io/doc-v2.4/user-doc/html/_m_e_t_a_d.html

that the interval keyword only works for 1D CVs. So if you have a multi-dimensional CV, the interval keyword will not work. 

A work around might be to add soft walls at the CV edges or reduce the amount of energy being added so that the system is unlikely to cross-over into those regions. 

Cheers,

Muneeb

[cecil...@gmail.com]

Hi Muneeb,

I get this error message:

+++ message: ERROR in input to action METAD with label meta : cannot understand the following words from the input line : UPPER_WALLS, ARG=antibeta.lessthan, AT=10.0, KAPPA=1000, LABEL=uwall,

Aborted

I get the same error if I try to use the keyword INTERVAL. This is my plumed file:


MOLINFO STRUCTURE=neh2.pdb
WHOLEMOLECULES ENTITY0=1-319
DUMPATOMS FILE=dump.xyz ATOMS=1-319

ANTIBETARMSD RESIDUES=all TYPE=DRMSD LESS_THAN={RATIONAL R_0=0.8 NN=8 MM=12} LABEL=antibeta STRANDS_CUTOFF=1

GYRATION TYPE=RADIUS ATOMS=1-319 LABEL=rgyr

METAD ...
   LABEL=meta
   ARG=antibeta.lessthan,rgyr SIGMA=0.1,0.05 HEIGHT=2.5 PACE=2500
   BIASFACTOR=15 TEMP=310
   UPPER_WALLS, ARG=antibeta.lessthan, AT=10.0, KAPPA=1000, LABEL=uwall
... METAD
PRINT ARG=antibeta.lessthan,rgyr STRIDE=500 FILE=COLVAR

[Carlo Camilloni]

Hi

UPPER_WALLS is not an option of METAD but an action itself, double check your input with the manual

Carlo

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[cecil...@gmail.com]

Thank you so very much. My metadynamics run started without problems after moving that line before the metad instructions.