[gmx-users] Rupture force definition

[Rakesh Mishra]

Dear Justin,

Can you explain something regarding this issue.

I couldn't get  resolve one  problem.  Though now I am able to make
restrict (immobile )
the needed residue and pulled another one.
But the contradiction that i am facing is that, when I am pulling with
-rate (in negative z direction, as I want to pull
the residue in the negative Z direction of box ) given below.
Still there we see  that pulling group is not moving the -ve direction of
z.


pull                           = yes
pull_ngroups              = 2
pull_ncoords              = 1
pull_group1_name          = chain-A-start
pull_group2_name          = chain-B-end
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 per 1 ns
pull_coord1_k                = 1000          ; kJ mol^-1 nm^-2
pull_coord1_start           = yes           ; define initial COM distance >
0


Best



On Tue, Feb 6, 2018 at 1:54 PM, Rakesh Mishra <rockinbhu at gmail.com> wrote:

> 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 <094736%2062491>, +91877749632*
>



-- 
* 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*