Creating Plumed.dat for two Collective variables ( distance and dihedral)

[Vikas Dubey]

Hi everyone, 

I am new to the plumed and interested in performing WT-metadynamics. I am trying to create a 2-CV plumed.dat file for my system. 

CV1 : distance between center_of_mass( 1,2,3,9,15,21) and center_of_mass( 1757,1758,1759,1766)  ( I want to vary the this distance from 10 to 17) 

CV2 : dihedral angle (1,2,1757,175)  ( at each distance I I want to vary the dihedral from -180 to 180)

I have created the following plumed.dat file. 

----------------------------------------------------------------------------------------------------------

phi: TORSION ATOMS=1,2,1757,1759

metad: METAD ARG=phi PACE=500 HEIGHT=1.2 SIGMA=0.35 FILE=HILLS BIASFACTOR=6.0 TEMP=310.0

first: COM ATOMS=1,2,3,9,15,21

last: COM ATOMS=1757,1758,1759,1766

comdist: DISTANCE ATOMS=first,last

UPPER_WALLS ARG=comdist AT=17.0 KAPPA=150.0 EXP=2 EPS=1 OFFSET=0 LABEL=uwall

LOWER_WALLS ARG=comdist AT=10.0 KAPPA=150 EXP=2 EPS=1 OFFSET=0 LABEL=lwall

UPPER_WALLS ARG=phi AT=pi  KAPPA=150.0 EXP=2 EPS=1 OFFSET=0 LABEL=uwall_2

LOWER_WALLS ARG=phi AT=pi KAPPA=150 EXP=2 EPS=1 OFFSET=0 LABEL=lwall_2

PRINT ARG=comdist, phi,metad.bias STRIDE=1 FILE=colvar

ENDPLUMED

----------------------------------------------------------------------------------------------------------

Does it look correct ? Is there any problem with this dat file ?  

Thanks,

Vikas

[Massimiliano Bonomi]

Dear Vikas,

I see a number of potential issues with this input file:

1) you are doing WT-metadynamics only in the dihedral CV. Is this what you want to do, or you want
to use also the distance between centers of mass as CV?

2) you don’t need lower and upper walls for the dihedral. And in any case these are set to the same value, phi.

3) please keep in mind that the unit of measure for distances is nanometers.

4) please look at the manual to deal with PBC and COM calculation, in case your system is periodic

Max

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[Vikas Dubey]

Dear Sir, 

Thanks a lot for your reply. I wanted to use both distance and dihedral angles as CV's. Sorry for the wrong input. I have corrected my file based on your suggestions. 

---------------------------------------------------------------------------------------------------------------------- 

phi: TORSION ATOMS=1,2,1757,1759

first: COM ATOMS=1,2,3,9,15,21

last: COM ATOMS=1757,1758,1759,1766

comdist: DISTANCE ATOMS=first,last

 metad: METAD ARG=phi,comdist PACE=500 HEIGHT=1.2 SIGMA=0.35,0.35 FILE=HILLS BIASFACTOR=6.0 TEMP=310.0

 UPPER_WALLS ARG=comdist AT=1.70 KAPPA=150.0 EXP=2 EPS=1 OFFSET=0 LABEL=uwall

 LOWER_WALLS ARG=comdist AT=1.0 KAPPA=150 EXP=2 EPS=1 OFFSET=0 LABEL=lwall

 PRINT ARG=comdist, phi,metad.bias STRIDE=1 FILE=colvar


 ENDPLUMED

----------------------------------------------------------------------------------------------------------------------------

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[Vikas Dubey]

Dear sir, 

Thanks for your suggestions.Final plumed file looks like this:

--------------------------------------------------------------------------------------------------------

 set up two variables for Phi angles

phi: TORSION ATOMS=1,2,1757,1759

first: COM ATOMS=1955,1956,1957,1958,1964,1970

last: COM ATOMS=1724,1725,1726,1733

comdist: DISTANCE ATOMS=first,last

metad: METAD ARG=comdist,phi PACE=500 HEIGHT=1.2 SIGMA=0.35,0.35 FILE=HILLS BIASFACTOR=6.0 TEMP=310.0

UPPER_WALLS ARG=comdist AT=1.70 KAPPA=150.0 OFFSET=0 LABEL=uwall

LOWER_WALLS ARG=comdist AT=1.0 KAPPA=150.0   OFFSET=0 LABEL=lwall

PRINT ARG=comdist,phi,metad.bias STRIDE=1 FILE=colvar

-----------------------------------------------------------------------------------------------

output data in colvar files look weird to me since comdist is in the range of 2-3 but I wanted to setup this distance in between of  1-1.7 (see bold tex). I have tried increasing value of KAPPA to 500. No changes. Why is this happening? Am I missing something?

#! FIELDS time comdist phi metad.bias

#! SET min_phi -pi

#! SET max_phi pi

 0.000000 2.384900 0.408712 0.000000

 0.002000 2.384803 0.425227 0.000000

 0.004000 2.384541 0.494223 0.000000

 0.006000 2.384081 0.601062 0.000000

 0.008000 2.383408 0.729541 0.000000

 0.010000 2.382535 0.856231 0.000000

 0.012000 2.381503 0.956213 0.000000

[Massimiliano Bonomi]

As I mentioned in my previous email, if your system is periodic, you have to be a bit careful when using COM. If this is the case, please have a look at the PLUMED manual for the COM directive, where you can find all the instructions.

As additional note, the sigma value for the distance CV might not be optimal. The value you are using seems a bit too large to me.

Max

Sent from my Nexus. Please excuse typos and brevity.

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