[gmx-users] gmx wham (again)

[Alex]

> This is the exact situation that the "cylinder" pull geometry is 
> designed to model. I suggest going that route rather than ad hoc 
> restraints, which will influence the PMF and should be otherwise 
> accounted for.
>
> -Justin
>
Hi Justin,

Thanks. To make sure things are more or less reasonable, I'd like to 
double-check with you... Here is what I have at the moment:

***
pull                 = yes
pull-coord1-type     = umbrella
pull_ngroups            = 2
pull_ncoords            = 1
pull_group1_name        = K
pull_group2_name        = CNT
pull_coord1_geometry    = distance      ; simple distance increase
pull-group2-pbcatom     = 1343
pull_coord1_groups      = 1 2
pull-coord1-dim         = N N Y
pull_coord1_rate        = 0.0
pull_coord1_k           = 1000          ; kJ mol^-1 nm^-2
pull_coord1_start       = yes           ; define initial COM distance > 0
***

Per your suggestion, I am changing this to:

***
pull                 = yes
pull-coord1-type     = umbrella
pull_ngroups            = 2
pull_ncoords            = 1
pull_group1_name        = K
pull_group2_name        = CNT
*pull_coord1_geometry    = cylinder      ; cylindrical sampling region**
**pull-cylinder-r         =  0.75 ; 1.5 nm cylinder diameter*
pull-group2-pbcatom     = 1343
pull_coord1_groups      = 1 2
pull-coord1-dim         = N N Y
pull_coord1_rate        = 0.0
pull_coord1_k           = 1000          ; kJ mol^-1 nm^-2
pull_coord1_start       = yes           ; define initial COM distance > 0
***

Everything else, including the bias, remains the same, though I am 
suspecting the pull-group2-pbcatom may no longer be needed. Does this 
seem reasonable?

Thank you,

Alex