[gmx-users] Pull Code: direction-periodic with 3 dimensions

[Justin Lemkul]

On 8/11/17 5:02 PM, Daniel Kozuch wrote:
> Hello,
> 
> I am using a pull code to increase the end-to-end distance of a protein
> (included below). I am using direction-periodic and would like the distance
> between the COM groups to be calculated in three dimensions. However,
> setting pull_coord1_dim = Y Y Y appears to have no effect and the distance
> printed to the pull file is still only in the pull_vec dimension (as
> verified by checking with gmx distance). Is there any way to use
> pull_coord1_dim = Y Y Y with direction-periodic?
> 

No, because direction and direction-periodic only use pull_coord1_vec.

http://manual.gromacs.org/documentation/2016.3/user-guide/mdp-options.html#com-pulling

-Justin

> pull                    = yes
> pull_ngroups            = 2
> pull_ncoords            = 1
> pull_group1_name        = Chain_Begin
> pull_group2_name        = Chain_End
> pull_coord1_type        = umbrella      ; harmonic biasing force
> pull_coord1_geometry    = direction-periodic
> pull_coord1_groups      = 1 2
> pull_coord1_dim         = Y Y Y
> pull_coord1_rate        = 0.0
> pull_coord1_k           = 5000          ; kJ mol^-1 nm^-2
> pull_coord1_start       = no           ; define initial COM distance > 0
> pull_coord1_init = 3.5
> pull_coord1_vec         = 0 0 1
> 
> 
> Thanks,
> Dan
> 

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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