[gmx-users] Use pull code to restrain the COM

[Bin Liu]

Hi All,

I would like to restrain the COM of a molecule, say a protein, in my
simulation. I found the pull code can do the job. However, I am not sure
about several parameters in the .mdp file.

For example, if I want to restrain the COM of the protein in only z
direction, but not rigidly, I can specify the following parameters:

*; Setting A*
*pull            = umbrella*
*pull-geometry   = position*
*pull-dim        = N N Y ; only applied to Z direction*
*pull-ngroups    = 1
*
*pull-group1     = Protein*
*pull-start      = no*
*pull-init1      = 3.0 3.0 3.0  ; suppose the initial position of the COM
is 3.0 3.0 3.0*
*pull-k1         = 50*

I am not confident about my understanding of the settings. Here I didn't
specify *pull-group0*. Therefore the position of the reference point is 0.0
0.0 0.0. But *pull-init1* moves the reference point to *3.0 3.0 3.0.  *I
don't know the reasonable range for *pull-k1 *too. I want the COM can only
have a small deviation from its initial position. Is 50 too large or too
small?

And I figured out another approach.

*; Setting B*
*pull            = umbrella*
*pull-geometry   = position*
*pull-dim        = N N Y ; only applied to Z direction*
*pull-ngroups    = 1
*
*pull-group1     = Protein*
*pull-start      = yes*
*pull-k1         = 50*
*
*
The GROMACS manual says *pull-start=yes *adds the COM distance of the
starting conformation to *pull-init. *Does it mean Setting B is equivalent
to Setting A? If I set *pull-geometry= position, *does *pull-start=yes *add
the initial position of the COM to *pull-init* as a vector? If it's true,
then I don't need to calculate the initial position of the COM.

Thanks a lot.

Best

Bin