[gmx-users] Rupture force definition

[Justin Lemkul]

On 2/14/18 7:31 AM, Rakesh Mishra wrote:
> 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.

Your settings are right, so either you need a larger force constant to 
induce the motion or you need to wait longer for the restoring forces in 
the system (whatever they are) to be overcome by the biasing potential.

-Justin

>
> 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*
>>
>
>

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

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

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