[gmx-users] Rupture force definition

[Justin Lemkul]

On 2/1/18 7:59 AM, Rakesh Mishra wrote:
> Dear Justin
>
> Here I am applying pull for two groups with respect to two reference group
> as following.
> ; Pull code
> pull                    = yes
> pull_ngroups            = 4
> pull_ncoords            = 1
> pull_group1_name        = chain_A8     (reference  also immobile )
> pull_group2_name        = chain_B35   (pulling group)
> pull_group3_name        = chain_A17    (reference also immobile)
> pull_group4_name        = chain_B26    (pulling)
> pull_coord1_type        = umbrella      ; harmonic biasing force
> pull_coord1_geometry    = distance      ; simple distance increase
> pull_coord1_groups      = 1 2
> pull_coord1_dim         = N N Y
> pull_coord1_rate        = 0.01          ; 0.01 nm per ps = 10 nm per 1 ns
> pull_coord1_k           = 1000          ; kJ mol^-1 nm^-2
> pull_coord1_start       = yes           ; define initial COM distance > 0
>
> In above protocol I want to make two reference group  as
> 1-chain_A8   2- chain_A17
> and two pull group.
> 1- chain_B35  2- chain_B26

You've defined four groups but then only used two, so you only get the 
effect of one reaction coordinate.

What you need to do is define the pull settings for all reaction 
coordinates simultaneously, e.g.:

pull                    = yes
pull_ngroups            = 4
pull_ncoords            = 2
pull_group1_name        = chain_A8
pull_group2_name        = chain_B35
pull_group3_name        = chain_A17
pull_group4_name        = chain_B26
; definition of reaction coordinate 1, groups 1-2
pull_coord1_type        = umbrella
pull_coord1_geometry    = distance
pull_coord1_groups      = 1 2
pull_coord1_dim         = N N Y
pull_coord1_rate        = 0.01
pull_coord1_k           = 1000
pull_coord1_start       = yes
; definition of reaction coordinate 2, groups 3-4
pull_coord2_type        = umbrella
pull_coord2_geometry    = distance
pull_coord2_groups      = 3 4
pull_coord2_dim         = N N Y
pull_coord2_rate        = 0.01
pull_coord2_k           = 1000
pull_coord2_start       = yes

Note that above I changed pull_ncoords to be set to 2, because you want 
two reaction coordinates. Then just specify the settings for each one, 
calling the appropriate groups by their assigned numbers.

-Justin

-- 
==================================================

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

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html

==================================================