Bug with CENTER_OF_MULTICOLVAR

[Alexandre Oliveira]

Dear all,
I’m simulating the permeation process of a solute through a membrane by Transition tempered metadynamics, using Plumed 2.5.7 with GROMACS 2019.4. For that purpose, I’m using two CVs. The first CV is the distance between the COM of the solute and the COM of the lipids inside a cylinder centered by the COM of the solute. The second CV is the coordination number between the solute and all the atoms of the lipids (excepts the Hydrogens) inside that cylinder. This is my input:

WHOLEMOLECULES ENTITY0=26927-26979
Solute: COM NOPBC ATOMS=26927-26979
all_non_hydrogen_POPC: GROUP NDX_FILE=index.ndx NDX_GROUP=POPC_&_!H*

density: DENSITY SPECIES=all_non_hydrogen_POPC
inside_cylinder: INCYLINDER ATOM=Solute DATA=density DIRECTION=Z RADIUS={TANH D_0=0 R_0=1.5} LOWMEM
COM_cylinder: CENTER_OF_MULTICOLVAR DATA=inside_cylinder
COM_cylinder_distance_1: DISTANCE ATOMS=Solute,COM_cylinder SCALED_COMPONENTS
SCALED_COMPONENTS


m: METAD ...
ARG=COM_cylinder_distance_1.c,inside_cylinder
PACE=2500
HEIGHT=1.3  
SIGMA=0.02,30.0
TTBIASTHRESHOLD=10.0
FILE=HILLS1
TTBIASFACTOR=30
TRANSITIONWELL0=0.0,420
TRANSITIONWELL1=0.48,0
TEMP=310.15
GRID_WSTRIDE=2500000
GRID_WFILE=grid1.dat
GRID_NOSPLINE
STORE_GRIDS
GRID_MIN=-0.5,0
GRID_MAX=+0.5,1000
GRID_BIN=200,5000
... m:

ARG=COM_cylinder_distance_1.c,inside_cylinder,m.bias FILE=COLVAR1

However, in the Plumed manual, I find a bug report for the CENTER_OF_MULTICOLVAR, in all recent versions of PLUMED “bug: The virial contribution for this type of virtual atom is not currently evaluated so do not use in bias functions unless the volume of the cell is fixed”. Everybody simulates these systems in the NPT ensemble so using the NVT ensemble is not an option. Do you have any suggestion to circumvent this issue or to define the CV in another way? Is this issue critical? Are you planning to evaluate the virial contribution in bias functions soon? If I create a new virtual atom from the virtual atom defined by CENTER_OF_MULTICOLVAR, something like this:

density: DENSITY SPECIES=all_non_hydrogen_POPC
inside_cylinder: INCYLINDER ATOM=Solute DATA=density DIRECTION=Z RADIUS={TANH D_0=0 R_0=1.5} LOWMEM
COM_cylinder: CENTER_OF_MULTICOLVAR DATA=inside_cylinder
COM_cylinder_coord: COM NOPBC ATOMS=COM_cylinder
COM_cylinder_distance_2: DISTANCE ATOMS=Solute,COM_cylinder_coord SCALED_COMPONENTS

Will I circumvent the issue?

Thanks for your attention, best wishes,

Alexandre Oliveira

[Gareth Tribello]

Hello 

You could try and see if it works with the hack-the-tree branch of PLUMED instead.  You can get this version of PLUMED by doing

git clone https://github.com/plumed/plumed2.git

git checkout hack-the-tree

You will need to change your input a bit.  This becomes:

density: GROUP ATOMS=all_non_hydrogen_POPC 

inside_cylinder: INCYLINDER CENTER=Solute ATOMS=density DIRECTION=Z RADIUS={TANH D_0=0 R_0=1.5}

COM_cylinder: CENTER ATOMS=all_non_hydrogen WEIGHTS=inside_cylinder

I think the rest should work though.  If you have any difficulties drop me an email and I can help you get set up.

I hope this helps

Gareth

COM_cylinder: CENTER_OF_MULTICOLVAR DATA=inside_cylinder
COM_cylinder_coord: COM NOPBC ATOMS=COM_cylinder
COM_cylinder_distance_2: DISTANCE ATOMS=Solute,COM_cylinder_coord SCALED_COMPONENTS

--
You received this message because you are subscribed to the Google Groups "PLUMED users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to plumed-users...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/plumed-users/877c923a-5a24-409d-be88-ee712500a184n%40googlegroups.com.

[Alexandre Oliveira]

Thank you for the suggestion.

Where can I get the hack-the-tree documentation, to learn the syntax?

Thank you in advance,

Best regards,

Alexandre Oliveira

[Gareth Tribello]

You can build the documentation using by doing

cd plumed2/user-doc

make doc

The documentation is not particularly complete yet though as it is a development branch.  If you want I can help you get your calculation setup.  If you send me your current plumed input and a few example frames I can help you get the new calculation setup.

I hope this helps

Gareth

To view this discussion on the web visit https://groups.google.com/d/msgid/plumed-users/be32288f-0d5b-41fa-8fe3-c89333b5f542n%40googlegroups.com.

[Alexandre Oliveira]

I found a way around using ZDISTANCE and INCYLINDER. For now, I won't be needing the hack-the-tree version.

Thank you for the help.

Best regards,

Alexandre Oliveira