contact map based path CVs in plumed 2

[Pratyush Tiwary]

Dear developers

Is it possible to use contact map based path CVs in plumed 2? I could not find any example input files online hence I ask.

Thanks a lot!

Pratyush

[Gareth Tribello]

You could do it using the PATH action.  This allows you to construct a PATH in an arbitrary metric.  You would thus define a set of arguments (in your case a set of coordination numbers for each of the contacts.  You create a pdb file containing the values of each of your contact in the frame (here you have a to use a special plumed format for the PDB so that you can specify the values of the arguments) and then you create a PATH using the EUCLIDEAN metric.

If you want I can dig around for you and see if I can setup an example.

Gareth

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[Pratyush Tiwary]

Thanks a lot Gareth! Examples would of course be very useful. The section on PATH does not have any examples yet, but I am guessing it should be similar to PATHMSD?

I will try it out myself and consult with you if it does not work out.

Pratyush

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[Carlo Camilloni]

I think that alternatively you can use CONTACTMAP with the CMDIST keyword and FUNCPATHMSD, in this way you can move the input files of plumed1 to plumed2 in an almost transparent way.

I have uploaded the example now on the git.

Carlo

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[Gareth Tribello]

Hello

Here is an example for the PATH option:

COORDINATION GROUPA=1 GROUPB=2 SWITCH={RATIONAL R_0=1.0} LABEL=d1

COORDINATION GROUPA=3 GROUPB=4 SWITCH={RATIONAL R_0=1.0} LABEL=d2

PATH REFERENCE=mypath.pdb TYPE=EUCLIDEAN LAMBDA=500 LABEL=pp

PRINT ARG=pp.* FILE=colvar

Your reference file should then look like

DESCRIPTION: my path in contact map space

REMARK WEIGHT=1.0 

REMARK ARG=d1,d2 

REMARK d1=1.0 d2=1.0

END

REMARK WEIGHT=1.0 

REMARK ARG=d1,d2 

REMARK d1=0.0 d2=1.0

END

This is for a two frame path using two contact and in which the values of the contacts at the various points in the path are 1.0,1.0 and 0.0,1.0.

Easy

Gareth

PS

I am not sure the FUNCPATHMSD option will work as it gives an error in the constructor if the actions in the function are not of RMSD type.

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[Pratyush Tiwary]

That is easy! Thanks a lot Gareth, it seems to work for me with plumed 2.1. I will be comparing some test cases with plumed 1.3 to make sure, but I doubt if there will be differences.

Pratyush

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[Carlo Camilloni]

Yes I have changed the code so that  FUNCPATHMSD can also work with contact map

Carlo

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