On 2/15/18 4:13 AM, Rakesh Mishra wrote:
Dear Justin thanks for your advise.
I will check for longer run for getting response according to you.
I would like to explain my system,which is siRNA of chain A and B.
Here, after doing all formalities, I had run 10 ns then try to apply the
pull protocol.
See, here for pulling this system, I have restricted 1st residue of
chain-A, and pulling last ( 22th)
residue of chain-B, which is at the same side end just below the 1st
residue of chain-A.
( means, both reference and pull groups are at the same end side ).
Note- I am pulling this 22th residue of chain-B in the downward (-z)
direction with negative rate.
( here pull group is below from the reference group)
I also followed your advise to pull with negative rate with high spring
constant. But in this case also,
system is not moving in the downwards (-z ) direction.
Interesting-
But the most interesting case is that for the same system just discussed
above, when I am
applying pulling code with + rate even with smaller spring constant, then
system is moving in
downward (-z) direction. While In my thinking, because I have given +rate,
so it should move in
the + z direction. So, could it be possible that there is one thing that
can also matter ,
i.e. whether, pull group is below and reference group is above .
Because in the same system, when I pull 22the residue of chain-A w.r.t
reference residue 1 of chain-B
(which is slightly below from the pull residue 22th of chain-A) with the
same +rate and spring constant.
In this case pull group moves in the + z direction (upward), which I expect
( note- here pull group is
slightly above from the reference group)
So, this contradiction with effect based on the end side pulling and posing
of reference and pull groups
is making it surprise and trouble.
How is the RNA oriented? Is the z-axis coincident with the helical axis?
If so, that's a poor choice for a reaction coordinate and you should
choose a different axis, orthogonal to the helix. Or just pull in all
dimensions so that it's the total COM distance between the base pair.
Remember, the tutorial is a special case in which a one-dimension pull
made sense due to the inherent geometry of the unidirectional growth
model of amyloid fibrils. Do not assume that all system should be
treated this way.
The negative pull rate means "bring the two specified groups together"
not necessarily "pull along -z" so be sure your orientation convention
aligns with what you're trying to do.
-Justin
On Wed, Feb 14, 2018 at 7:53 PM, Justin Lemkul <jalem...@vt.edu> wrote:
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 sett
<https://maps.google.com/?q=n+coordinates.+Then+just+specify+the+sett&entry=gmail&source=g>ings
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*
--
==================================================
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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/Mailing_Lists/GMX-Users_List before posting!
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* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
send a mail to gmx-users-requ...@gromacs.org.
--
==================================================
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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http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
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