[gmx-users] Rupture force definition

[Rakesh Mishra]

Thank you very much Justin.

Here it is working but having some  problem.
pull_group2_name = chain_B35  is moving in the + z direction &
pull_group4_name= chain_B26   is  moving oppositely in the -z direction
While I have given pull in +z direction for both the above group.

Note - pull_group1_name = chain_A8 and  pull_group3_name  = chain_A17 are
immobile here as well as acting as reference.


On Thu, Feb 1, 2018 at 7:16 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
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-- 
* Rakesh Kumar Mishra*
*  (RA)CSD  SINP Kolkata, India*

*E-mail - rakesh.mishra at saha.ac.in <rakesh.mishra at saha.ac.in> *

*Phone n. +91 9473662491, +91877749632*