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 <rockin...@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 <jalem...@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
jalem...@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.mis...@saha.ac.in <rakesh.mis...@saha.ac.in> *
*Phone n. +91 9473662491 <094736%2062491>, +91877749632*
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==================================================
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
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