Metadynamics with restraint bias on other different CVs

[lzzhe...@gmail.com]

Hi plumed users,

I am planning  to simulate a protein with about 250 amino acid. One of the protein helix is in different position when different ligands bind. 

So I am considering using CVs from the helix part. For example, the C alpha contact map between the helix and other part of the protein. 

When I use the standard well-tempered metadynamics on the contact map cv, the 2nd structure of the helix may be distorted. In this case, could I add restraint bias on the helix 2nd structure by a cv using AlphaRMSD with upper_walls and lower_walls?  In this way, I could use metadynamics sampling the helix position in the same time keeping the 2^nd structure untouched.

Eg. here could be part of the plumed.dat input file

############## plumed.dat ##################

cv1: CONTACTMAP ......

helix: ALPHARMSD RESIDUES=25-40  ......

UPPER_WALL  ARG=helix ......

LOWER_WALL ARG=helix ......

metad: METAD  ARG=cv1 ......  TEMP=300.0

PRINT ARG=cv1, metad.bias ......

############## plumed.dat ##################

So, is this a good idea?  Is there any other good cvs?

Or do you have any suggestion?

Best regards!

Liangzhen

[Fabrizio Marinelli]

Dear Liangzhen,

that sounds a good way to go, you can definitely use an upper wall on AlphaRMSD.
Another possibility is to use a path collective variable in which endpoints and intermediate points have the helix you mentioned not distorted.

Best,

Fabrizio

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[ZHENG LIANGZHEN]

Hi Fabrizio,

Thank you for the valuable suggestions. 

I have another question about the bias added on the helix structure. This bias added on the helix 2nd structure is in a way different from the gaussian added in metadynamics. 

When I analyze the data, how to treat the bias part on the helix structure? Using different way to reweight the cvs? You have any recommended reference papers or materials?

Thanks a lot. 

Best regards!

Liangzhen

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