WHOLEMOLECULES not recognizing atoms, throws "no atom found for WHOLEMOLECULES!" error.

[manuv...@gmail.com]

Hi,

I am trying to use PLUMED for a metadynamics run of a membrane protein involving a function of COM as the CV. In order to ensure that the drift of my protein outside the PBC does not affect my value of COM I am giving the WHOLEMOLECULES directive to PLUMED. (WHOLEMOLECULES ENTITY=1-1246). However, when I pass this directive plumed shows an error - "no atom found for WHOLEMOLECULES!". Surprisingly it throws no error when I try to calculate the COM of these atoms which means that it is recognizing these atoms. I checked the source for WHOLEMOLECULES and the exception is thrown if the number of atoms in the group is 0, which is not the case here.

I am also calculating some angles later so I really need to get WHOLEMOLECULES working. Please suggest a solution for this issue. I don't know if it matters with this problem but I am using MARTINI with gromacs to simulate this system.


Versions tried: PLUMED - 2.13, 2.2b. GROMACS - 5.0.6

Regards,
Manu Vajpai
PhD Candidate
Department of Biological Sciences and Bioengineering
IIT Kanpur

[Gareth Tribello]

Hello

I think you need to use either ENTITY0 or ENTITY1 rather than ENTITY.

Gareth

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[manuv...@gmail.com]

Thank you! That fixed the issue.

Regards,
Manu Vajpai