[gmx-users] Rupture force definition
rockinbhu at gmail.com
Tue Feb 6 09:24:10 CET 2018
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 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
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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*
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