Re: [gmx-users] Justin paper 2010 pulling

[Justin Lemkul]

On 9/19/18 6:01 AM, Rakesh Mishra wrote:

There is no rotation of helix.

But of course during the pulling, helical form of dna goes into stretched
form and then one strand start to slide on
  another strand. During  this, slight fluctuation on the motion of helical
axis
occurs., which is obvious otherwise how to pull.

Or
If I want for some advise from you that. I want to pull one strand of
dsDNA  along
its helical axis to separate the both strand  then what will be Gromacs
protocol of pulling.


It seems to me you have two steps to perform:

1. Extend the duplex to a "ladder-like" conformation
2. Slide one strand past the other

In step 1, I would set the reaction coordinate to be the vector 
connecting the terminal *base pairs* (not just one base in one DNA 
chain) and pull along that vector in all dimensions. The force will 
primarily act in one Cartesian dimension, but by doing it this way, you 
never have to assume (or hope) that your system stays nicely aligned 
along one axis. The pulling will take some time, and rotation to some 
extent is inevitable.


In step 2, once the duplex is fully extended, you should be able to do 
what you were proposing before, using the terminal single base of each 
DNA strand. Again, I still think it's problematic to assume a biasing 
force in only one dimension, but that's for you to test.


I'm sorry that I don't have time to look at all the files you sent 
off-list or read all the papers you linked. But this is what I can offer 
as a suggestion. It's a very difficult system to deal with.


-Justin





On Mon, Sep 17, 2018 at 6:42 PM, Justin Lemkul  wrote:



On 9/17/18 8:50 AM, Rakesh Mishra wrote:


In my above protocol,

What I found that, my system (12 dsDNA) placed with their helical axis is
along the X  axis (in VMD we checked ).


If the helix rotates, your application of a bias only along x becomes
invalid or will do something you don't want.

When I am applying pulling on r_12  ( with  pull_coord1_dim = Y  N  N

). Keeping r_24 as a reference group (not fixed).
Distance between both group is increasing along X axis. In VMD it is
clearly showing that both the group are
moving in opposite direction along the helix ( X axis) direction. Which is
showing that r_24 is feeling equal pulling like r_12 (on which pulling is
applied)
in the opposite direction of biasing vector. i. e.  r_24 is moving in  -X
direction and r_12 is moving in +X direction.


Again, this is just a natural outcome of the biasing force being
interpolated onto the affected atoms.

-Justin



On Mon, Sep 17, 2018 at 6:00 PM, Justin Lemkul  wrote:



On 9/17/18 8:25 AM, Rakesh Mishra wrote:

Agreed with this

"Newtonian mechanics always apply, but it's not as simple as "pull on X,
and Y moves." Your system evolves under the influence of the biasing
force."

Perhaps my nomenclature was bad here - X and Y are not Cartesian

directions, they are the groups that you're specifying in the .mdp file
that define the vector of the pulling force.

The same I am saying that on  Pulling X, X will fell equal and opposite
but


not Y and  Z.

Correct.

Meaning ,


If 3' of one strand will Pull  along X then 3' (reference group , which
is
not fixed )of complimentary strand  will move opposite along X . while Y
and  Z
those where no biasing force are applied, so Y and Z are  free to move
in
random (any direction ).


Simple representation form your tutorial like.
In my thinking in this following protocol r_24 and r_12 will move
oppositely along X direction. But not Y and Z.

The problem here is the the groups *will not* necessarily "move

oppositely
along X." Your biasing force causes a net increase in the length of the
vector connecting r_12 and r_24. That's it. Perhaps that means one group
moves and the other oscillates in place. Maybe they do, in fact, move in
different directions. The net motion of any group depends on all of the
forces in the system. Maybe your biasing potential causes a local helical
unwinding, allowing water to enter in between the bases or the hydrogen
bonding structure changes, which then causes different diffusion in any
dimension. But the biasing force only ever applies along X.

-Justin


pull_ngroups   = 2


pull_ncoords   = 1
pull_group1_name= r_24 ; 3' of  chain B of dsDNA as a
reference gorup (not  fixed)
pull_group2_name= r_12  ;  3' of  chain A of dsDNA as a
pulling gorup
pull_coord1_type  = umbrella  ; harmonic biasing force
pull_coord1_geometry   = distance  ; simple distance increase
pull_coord1_groups   = 1  2
pull_coord1_dim   = Y  N  N
pull_coord1_rate  = 0.005  ; 0.005 nm per ps = 5nm per 1
ns
pull_coord1_k  = 1000  ; kJ mol^-1 nm^-2
pull_coord1_start = yes   ; define initial COM distance
0




On Mon, Sep 17, 2018 at 5:18 PM, Justin Lemkul  wrote:


On 9/17/18 4:52 AM, Rakesh Mishra wrote:

Agreed.


But, I could not solve.
  

Re: [gmx-users] Justin paper 2010 pulling

[Rakesh Mishra]

There is no rotation of helix.

But of course during the pulling, helical form of dna goes into stretched
form and then one strand start to slide on
 another strand. During  this, slight fluctuation on the motion of helical
axis
occurs., which is obvious otherwise how to pull.

Or
If I want for some advise from you that. I want to pull one strand of
dsDNA  along
its helical axis to separate the both strand  then what will be Gromacs
protocol of pulling.




On Mon, Sep 17, 2018 at 6:42 PM, Justin Lemkul  wrote:

>
>
> On 9/17/18 8:50 AM, Rakesh Mishra wrote:
>
>> In my above protocol,
>>
>> What I found that, my system (12 dsDNA) placed with their helical axis is
>> along the X  axis (in VMD we checked ).
>>
>
> If the helix rotates, your application of a bias only along x becomes
> invalid or will do something you don't want.
>
> When I am applying pulling on r_12  ( with  pull_coord1_dim = Y  N  N
>> ). Keeping r_24 as a reference group (not fixed).
>> Distance between both group is increasing along X axis. In VMD it is
>> clearly showing that both the group are
>> moving in opposite direction along the helix ( X axis) direction. Which is
>> showing that r_24 is feeling equal pulling like r_12 (on which pulling is
>> applied)
>> in the opposite direction of biasing vector. i. e.  r_24 is moving in  -X
>> direction and r_12 is moving in +X direction.
>>
>
> Again, this is just a natural outcome of the biasing force being
> interpolated onto the affected atoms.
>
> -Justin
>
>
>> On Mon, Sep 17, 2018 at 6:00 PM, Justin Lemkul  wrote:
>>
>>
>>> On 9/17/18 8:25 AM, Rakesh Mishra wrote:
>>>
>>> Agreed with this

 "Newtonian mechanics always apply, but it's not as simple as "pull on X,
 and Y moves." Your system evolves under the influence of the biasing
 force."

 Perhaps my nomenclature was bad here - X and Y are not Cartesian
>>> directions, they are the groups that you're specifying in the .mdp file
>>> that define the vector of the pulling force.
>>>
>>> The same I am saying that on  Pulling X, X will fell equal and opposite
>>> but
>>>
 not Y and  Z.

 Correct.
>>>
>>> Meaning ,
>>>
 If 3' of one strand will Pull  along X then 3' (reference group , which
 is
 not fixed )of complimentary strand  will move opposite along X . while Y
 and  Z
 those where no biasing force are applied, so Y and Z are  free to move
 in
 random (any direction ).


 Simple representation form your tutorial like.
 In my thinking in this following protocol r_24 and r_12 will move
 oppositely along X direction. But not Y and Z.

 The problem here is the the groups *will not* necessarily "move
>>> oppositely
>>> along X." Your biasing force causes a net increase in the length of the
>>> vector connecting r_12 and r_24. That's it. Perhaps that means one group
>>> moves and the other oscillates in place. Maybe they do, in fact, move in
>>> different directions. The net motion of any group depends on all of the
>>> forces in the system. Maybe your biasing potential causes a local helical
>>> unwinding, allowing water to enter in between the bases or the hydrogen
>>> bonding structure changes, which then causes different diffusion in any
>>> dimension. But the biasing force only ever applies along X.
>>>
>>> -Justin
>>>
>>>
>>> pull_ngroups   = 2
>>>
 pull_ncoords   = 1
 pull_group1_name= r_24 ; 3' of  chain B of dsDNA as a
 reference gorup (not  fixed)
 pull_group2_name= r_12  ;  3' of  chain A of dsDNA as a
 pulling gorup
 pull_coord1_type  = umbrella  ; harmonic biasing force
 pull_coord1_geometry   = distance  ; simple distance increase
 pull_coord1_groups   = 1  2
 pull_coord1_dim   = Y  N  N
 pull_coord1_rate  = 0.005  ; 0.005 nm per ps = 5nm per 1
 ns
 pull_coord1_k  = 1000  ; kJ mol^-1 nm^-2
 pull_coord1_start = yes   ; define initial COM distance
 >
 0




 On Mon, Sep 17, 2018 at 5:18 PM, Justin Lemkul  wrote:


 On 9/17/18 4:52 AM, Rakesh Mishra wrote:
>
> Agreed.
>
>> But, I could not solve.
>> So Justin, If I pull 3' end of one strand of DNA by taking as
>> 3' end of the complimentary strand as a reference group (Note that
>> I have not fixed or not made it immobile ) then according to the
>> theory
>> of
>> newtons third law reference group (which is not immobile or not fixed
>> )
>> will get
>> same equal and opposite pull and will move in the opposite direction.
>> am I correct.
>>
>> You set two groups that define a vector along which a biasing
>> potential
>>
> is
> applied. The net displacement of either of those groups (or any other
> atoms
> in the system) is a function of the total force acting on all of 

Re: [gmx-users] Justin paper 2010 pulling

[Justin Lemkul]

On 9/17/18 8:50 AM, Rakesh Mishra wrote:

In my above protocol,

What I found that, my system (12 dsDNA) placed with their helical axis is
along the X  axis (in VMD we checked ).


If the helix rotates, your application of a bias only along x becomes 
invalid or will do something you don't want.



When I am applying pulling on r_12  ( with  pull_coord1_dim = Y  N  N
). Keeping r_24 as a reference group (not fixed).
Distance between both group is increasing along X axis. In VMD it is
clearly showing that both the group are
moving in opposite direction along the helix ( X axis) direction. Which is
showing that r_24 is feeling equal pulling like r_12 (on which pulling is
applied)
in the opposite direction of biasing vector. i. e.  r_24 is moving in  -X
direction and r_12 is moving in +X direction.


Again, this is just a natural outcome of the biasing force being 
interpolated onto the affected atoms.


-Justin



On Mon, Sep 17, 2018 at 6:00 PM, Justin Lemkul  wrote:



On 9/17/18 8:25 AM, Rakesh Mishra wrote:


Agreed with this

"Newtonian mechanics always apply, but it's not as simple as "pull on X,
and Y moves." Your system evolves under the influence of the biasing
force."


Perhaps my nomenclature was bad here - X and Y are not Cartesian
directions, they are the groups that you're specifying in the .mdp file
that define the vector of the pulling force.

The same I am saying that on  Pulling X, X will fell equal and opposite but

not Y and  Z.


Correct.

Meaning ,

If 3' of one strand will Pull  along X then 3' (reference group , which is
not fixed )of complimentary strand  will move opposite along X . while Y
and  Z
those where no biasing force are applied, so Y and Z are  free to move in
random (any direction ).


Simple representation form your tutorial like.
In my thinking in this following protocol r_24 and r_12 will move
oppositely along X direction. But not Y and Z.


The problem here is the the groups *will not* necessarily "move oppositely
along X." Your biasing force causes a net increase in the length of the
vector connecting r_12 and r_24. That's it. Perhaps that means one group
moves and the other oscillates in place. Maybe they do, in fact, move in
different directions. The net motion of any group depends on all of the
forces in the system. Maybe your biasing potential causes a local helical
unwinding, allowing water to enter in between the bases or the hydrogen
bonding structure changes, which then causes different diffusion in any
dimension. But the biasing force only ever applies along X.

-Justin


pull_ngroups   = 2

pull_ncoords   = 1
pull_group1_name= r_24 ; 3' of  chain B of dsDNA as a
reference gorup (not  fixed)
pull_group2_name= r_12  ;  3' of  chain A of dsDNA as a
pulling gorup
pull_coord1_type  = umbrella  ; harmonic biasing force
pull_coord1_geometry   = distance  ; simple distance increase
pull_coord1_groups   = 1  2
pull_coord1_dim   = Y  N  N
pull_coord1_rate  = 0.005  ; 0.005 nm per ps = 5nm per 1
ns
pull_coord1_k  = 1000  ; kJ mol^-1 nm^-2
pull_coord1_start = yes   ; define initial COM distance >
0




On Mon, Sep 17, 2018 at 5:18 PM, Justin Lemkul  wrote:



On 9/17/18 4:52 AM, Rakesh Mishra wrote:

Agreed.

But, I could not solve.
So Justin, If I pull 3' end of one strand of DNA by taking as
3' end of the complimentary strand as a reference group (Note that
I have not fixed or not made it immobile ) then according to the theory
of
newtons third law reference group (which is not immobile or not fixed )
will get
same equal and opposite pull and will move in the opposite direction.
am I correct.

You set two groups that define a vector along which a biasing potential

is
applied. The net displacement of either of those groups (or any other
atoms
in the system) is a function of the total force acting on all of the
atoms.
Newtonian mechanics always apply, but it's not as simple as "pull on X,
and
Y moves." Your system evolves under the influence of the biasing force.

Your results are probably somewhat confounded by the fact that you're
pulling along a vector that is oblique to both the helical axis and the
hydrogen-bonding plane. It's not trivial to apply forces to duplex DNA,
so
judicious choice of pulling vector is critical.

-Justin



On Fri, Sep 14, 2018 at 5:11 PM, Justin Lemkul  wrote:


On 9/14/18 3:14 AM, Rakesh Mishra wrote:

Dear Dr. Justin,


Of course I agree with your points. There is no point to not believe
on
you,
that's why we are discussing and thanks for your comment.
I raised the question because I observed the problem .
And it was matter of just common sense for me that
why the change of saving frequency is affecting the much difference
in the maximum value of force curve in pulling along the axial
direction.

Let me clear again, I say Input parameters of the pull.mdp files are
same
for both the 

Re: [gmx-users] Justin paper 2010 pulling

[Rakesh Mishra]

In my above protocol,

What I found that, my system (12 dsDNA) placed with their helical axis is
along the X  axis (in VMD we checked ).
When I am applying pulling on r_12  ( with  pull_coord1_dim = Y  N  N
). Keeping r_24 as a reference group (not fixed).
Distance between both group is increasing along X axis. In VMD it is
clearly showing that both the group are
moving in opposite direction along the helix ( X axis) direction. Which is
showing that r_24 is feeling equal pulling like r_12 (on which pulling is
applied)
in the opposite direction of biasing vector. i. e.  r_24 is moving in  -X
direction and r_12 is moving in +X direction.


On Mon, Sep 17, 2018 at 6:00 PM, Justin Lemkul  wrote:

>
>
> On 9/17/18 8:25 AM, Rakesh Mishra wrote:
>
>> Agreed with this
>>
>> "Newtonian mechanics always apply, but it's not as simple as "pull on X,
>> and Y moves." Your system evolves under the influence of the biasing
>> force."
>>
>
> Perhaps my nomenclature was bad here - X and Y are not Cartesian
> directions, they are the groups that you're specifying in the .mdp file
> that define the vector of the pulling force.
>
> The same I am saying that on  Pulling X, X will fell equal and opposite but
>> not Y and  Z.
>>
>
> Correct.
>
> Meaning ,
>> If 3' of one strand will Pull  along X then 3' (reference group , which is
>> not fixed )of complimentary strand  will move opposite along X . while Y
>> and  Z
>> those where no biasing force are applied, so Y and Z are  free to move in
>> random (any direction ).
>>
>>
>> Simple representation form your tutorial like.
>> In my thinking in this following protocol r_24 and r_12 will move
>> oppositely along X direction. But not Y and Z.
>>
>
> The problem here is the the groups *will not* necessarily "move oppositely
> along X." Your biasing force causes a net increase in the length of the
> vector connecting r_12 and r_24. That's it. Perhaps that means one group
> moves and the other oscillates in place. Maybe they do, in fact, move in
> different directions. The net motion of any group depends on all of the
> forces in the system. Maybe your biasing potential causes a local helical
> unwinding, allowing water to enter in between the bases or the hydrogen
> bonding structure changes, which then causes different diffusion in any
> dimension. But the biasing force only ever applies along X.
>
> -Justin
>
>
> pull_ngroups   = 2
>> pull_ncoords   = 1
>> pull_group1_name= r_24 ; 3' of  chain B of dsDNA as a
>> reference gorup (not  fixed)
>> pull_group2_name= r_12  ;  3' of  chain A of dsDNA as a
>> pulling gorup
>> pull_coord1_type  = umbrella  ; harmonic biasing force
>> pull_coord1_geometry   = distance  ; simple distance increase
>> pull_coord1_groups   = 1  2
>> pull_coord1_dim   = Y  N  N
>> pull_coord1_rate  = 0.005  ; 0.005 nm per ps = 5nm per 1
>> ns
>> pull_coord1_k  = 1000  ; kJ mol^-1 nm^-2
>> pull_coord1_start = yes   ; define initial COM distance >
>> 0
>>
>>
>>
>>
>> On Mon, Sep 17, 2018 at 5:18 PM, Justin Lemkul  wrote:
>>
>>
>>> On 9/17/18 4:52 AM, Rakesh Mishra wrote:
>>>
>>> Agreed.

 But, I could not solve.
So Justin, If I pull 3' end of one strand of DNA by taking as
 3' end of the complimentary strand as a reference group (Note that
 I have not fixed or not made it immobile ) then according to the theory
 of
 newtons third law reference group (which is not immobile or not fixed )
 will get
 same equal and opposite pull and will move in the opposite direction.
 am I correct.

 You set two groups that define a vector along which a biasing potential
>>> is
>>> applied. The net displacement of either of those groups (or any other
>>> atoms
>>> in the system) is a function of the total force acting on all of the
>>> atoms.
>>> Newtonian mechanics always apply, but it's not as simple as "pull on X,
>>> and
>>> Y moves." Your system evolves under the influence of the biasing force.
>>>
>>> Your results are probably somewhat confounded by the fact that you're
>>> pulling along a vector that is oblique to both the helical axis and the
>>> hydrogen-bonding plane. It's not trivial to apply forces to duplex DNA,
>>> so
>>> judicious choice of pulling vector is critical.
>>>
>>> -Justin
>>>
>>>
>>>
>>> On Fri, Sep 14, 2018 at 5:11 PM, Justin Lemkul  wrote:


 On 9/14/18 3:14 AM, Rakesh Mishra wrote:
>
> Dear Dr. Justin,
>
>> Of course I agree with your points. There is no point to not believe
>> on
>> you,
>> that's why we are discussing and thanks for your comment.
>> I raised the question because I observed the problem .
>> And it was matter of just common sense for me that
>> why the change of saving frequency is affecting the much difference
>> in the maximum value of force curve in pulling along the axial
>> 

Re: [gmx-users] Justin paper 2010 pulling

[Justin Lemkul]

On 9/17/18 8:25 AM, Rakesh Mishra wrote:

Agreed with this

"Newtonian mechanics always apply, but it's not as simple as "pull on X,
and Y moves." Your system evolves under the influence of the biasing force."


Perhaps my nomenclature was bad here - X and Y are not Cartesian 
directions, they are the groups that you're specifying in the .mdp file 
that define the vector of the pulling force.



The same I am saying that on  Pulling X, X will fell equal and opposite but
not Y and  Z.


Correct.


Meaning ,
If 3' of one strand will Pull  along X then 3' (reference group , which is
not fixed )of complimentary strand  will move opposite along X . while Y
and  Z
those where no biasing force are applied, so Y and Z are  free to move in
random (any direction ).


Simple representation form your tutorial like.
In my thinking in this following protocol r_24 and r_12 will move
oppositely along X direction. But not Y and Z.


The problem here is the the groups *will not* necessarily "move 
oppositely along X." Your biasing force causes a net increase in the 
length of the vector connecting r_12 and r_24. That's it. Perhaps that 
means one group moves and the other oscillates in place. Maybe they do, 
in fact, move in different directions. The net motion of any group 
depends on all of the forces in the system. Maybe your biasing potential 
causes a local helical unwinding, allowing water to enter in between the 
bases or the hydrogen bonding structure changes, which then causes 
different diffusion in any dimension. But the biasing force only ever 
applies along X.


-Justin


pull_ngroups   = 2
pull_ncoords   = 1
pull_group1_name= r_24 ; 3' of  chain B of dsDNA as a
reference gorup (not  fixed)
pull_group2_name= r_12  ;  3' of  chain A of dsDNA as a
pulling gorup
pull_coord1_type  = umbrella  ; harmonic biasing force
pull_coord1_geometry   = distance  ; simple distance increase
pull_coord1_groups   = 1  2
pull_coord1_dim   = Y  N  N
pull_coord1_rate  = 0.005  ; 0.005 nm per ps = 5nm per 1 ns
pull_coord1_k  = 1000  ; kJ mol^-1 nm^-2
pull_coord1_start = yes   ; define initial COM distance > 0




On Mon, Sep 17, 2018 at 5:18 PM, Justin Lemkul  wrote:



On 9/17/18 4:52 AM, Rakesh Mishra wrote:


Agreed.

But, I could not solve.
   So Justin, If I pull 3' end of one strand of DNA by taking as
3' end of the complimentary strand as a reference group (Note that
I have not fixed or not made it immobile ) then according to the theory of
newtons third law reference group (which is not immobile or not fixed )
will get
same equal and opposite pull and will move in the opposite direction.
am I correct.


You set two groups that define a vector along which a biasing potential is
applied. The net displacement of either of those groups (or any other atoms
in the system) is a function of the total force acting on all of the atoms.
Newtonian mechanics always apply, but it's not as simple as "pull on X, and
Y moves." Your system evolves under the influence of the biasing force.

Your results are probably somewhat confounded by the fact that you're
pulling along a vector that is oblique to both the helical axis and the
hydrogen-bonding plane. It's not trivial to apply forces to duplex DNA, so
judicious choice of pulling vector is critical.

-Justin




On Fri, Sep 14, 2018 at 5:11 PM, Justin Lemkul  wrote:



On 9/14/18 3:14 AM, Rakesh Mishra wrote:

Dear Dr. Justin,

Of course I agree with your points. There is no point to not believe on
you,
that's why we are discussing and thanks for your comment.
I raised the question because I observed the problem .
And it was matter of just common sense for me that
why the change of saving frequency is affecting the much difference
in the maximum value of force curve in pulling along the axial
direction.

Let me clear again, I say Input parameters of the pull.mdp files are
same
for both the simulation.
Only difference is the different saving frequency of position and energy
coordinates.
Please see below two cases

Case -A

 simulation of same system with same input parameter during pulling
1  nstxtcout= 2000   ; every 4 ps
   nstenergy= 5000

2  nstxtcout= 2000   ; every 4 ps
   nstenergy= 2000

  (output files, pullf1.xvg, and pullf2.xvg are different very much
w.r.t
peak value of force )
   Same thing happening also in the following below case, please see
this.

Case B.

1  nstxtcout= 2000   ; every 4 ps
   nstenergy   = 5000

2-  nstxtcout= 1000   ; every 4 ps
nstenergy   = 5000

Because, now this gromacs discussion user platform do not allow to
upload
any other data (eg, plot, pdf file etc) otherwise I can upload the plot.

You can always upload images to file-sharing services and provide links.

But first, watch the trajectories and see how they're behaving. The
systems are likely 

Re: [gmx-users] Justin paper 2010 pulling

[Rakesh Mishra]

Agreed with this

"Newtonian mechanics always apply, but it's not as simple as "pull on X,
and Y moves." Your system evolves under the influence of the biasing force."

The same I am saying that on  Pulling X, X will fell equal and opposite but
not Y and  Z.

Meaning ,
If 3' of one strand will Pull  along X then 3' (reference group , which is
not fixed )of complimentary strand  will move opposite along X . while Y
and  Z
those where no biasing force are applied, so Y and Z are  free to move in
random (any direction ).


Simple representation form your tutorial like.
In my thinking in this following protocol r_24 and r_12 will move
oppositely along X direction. But not Y and Z.

pull_ngroups   = 2
pull_ncoords   = 1
pull_group1_name= r_24 ; 3' of  chain B of dsDNA as a
reference gorup (not  fixed)
pull_group2_name= r_12  ;  3' of  chain A of dsDNA as a
pulling gorup
pull_coord1_type  = umbrella  ; harmonic biasing force
pull_coord1_geometry   = distance  ; simple distance increase
pull_coord1_groups   = 1  2
pull_coord1_dim   = Y  N  N
pull_coord1_rate  = 0.005  ; 0.005 nm per ps = 5nm per 1 ns
pull_coord1_k  = 1000  ; kJ mol^-1 nm^-2
pull_coord1_start = yes   ; define initial COM distance > 0




On Mon, Sep 17, 2018 at 5:18 PM, Justin Lemkul  wrote:

>
>
> On 9/17/18 4:52 AM, Rakesh Mishra wrote:
>
>> Agreed.
>>
>> But, I could not solve.
>>   So Justin, If I pull 3' end of one strand of DNA by taking as
>> 3' end of the complimentary strand as a reference group (Note that
>> I have not fixed or not made it immobile ) then according to the theory of
>> newtons third law reference group (which is not immobile or not fixed )
>> will get
>> same equal and opposite pull and will move in the opposite direction.
>> am I correct.
>>
>
> You set two groups that define a vector along which a biasing potential is
> applied. The net displacement of either of those groups (or any other atoms
> in the system) is a function of the total force acting on all of the atoms.
> Newtonian mechanics always apply, but it's not as simple as "pull on X, and
> Y moves." Your system evolves under the influence of the biasing force.
>
> Your results are probably somewhat confounded by the fact that you're
> pulling along a vector that is oblique to both the helical axis and the
> hydrogen-bonding plane. It's not trivial to apply forces to duplex DNA, so
> judicious choice of pulling vector is critical.
>
> -Justin
>
>
>
>> On Fri, Sep 14, 2018 at 5:11 PM, Justin Lemkul  wrote:
>>
>>
>>> On 9/14/18 3:14 AM, Rakesh Mishra wrote:
>>>
>>> Dear Dr. Justin,

 Of course I agree with your points. There is no point to not believe on
 you,
 that's why we are discussing and thanks for your comment.
 I raised the question because I observed the problem .
 And it was matter of just common sense for me that
 why the change of saving frequency is affecting the much difference
 in the maximum value of force curve in pulling along the axial
 direction.

 Let me clear again, I say Input parameters of the pull.mdp files are
 same
 for both the simulation.
 Only difference is the different saving frequency of position and energy
 coordinates.
 Please see below two cases

 Case -A

 simulation of same system with same input parameter during pulling
 1  nstxtcout= 2000   ; every 4 ps
   nstenergy= 5000

 2  nstxtcout= 2000   ; every 4 ps
   nstenergy= 2000

  (output files, pullf1.xvg, and pullf2.xvg are different very much
 w.r.t
 peak value of force )
   Same thing happening also in the following below case, please see
 this.

 Case B.

 1  nstxtcout= 2000   ; every 4 ps
   nstenergy   = 5000

 2-  nstxtcout= 1000   ; every 4 ps
nstenergy   = 5000

 Because, now this gromacs discussion user platform do not allow to
 upload
 any other data (eg, plot, pdf file etc) otherwise I can upload the plot.

 You can always upload images to file-sharing services and provide links.
>>>
>>> But first, watch the trajectories and see how they're behaving. The
>>> systems are likely just doing somewhat different things, as I said
>>> before.
>>> There is no reason to expect even the exact same .tpr file to produce the
>>> exact same output (binary identical), for reasons stated here:
>>> http://www.gromacs.org/Documentation/Terminology/Reproducibility
>>>
>>> Again, I emphasize that output control has no impact on the computation
>>> of
>>> forces or anything to do with the pull code. This cannot be the reason
>>> for
>>> differences in trajectories.
>>>
>>> -Justin
>>>
>>> On Thu, Sep 13, 2018 at 4:57 PM, Justin Lemkul  wrote:
>>>

 On 9/13/18 1:20 AM, Rakesh Mishra wrote:
>

Re: [gmx-users] Justin paper 2010 pulling

[Justin Lemkul]

On 9/17/18 4:52 AM, Rakesh Mishra wrote:

Agreed.

But, I could not solve.
  So Justin, If I pull 3' end of one strand of DNA by taking as
3' end of the complimentary strand as a reference group (Note that
I have not fixed or not made it immobile ) then according to the theory of
newtons third law reference group (which is not immobile or not fixed )
will get
same equal and opposite pull and will move in the opposite direction.
am I correct.


You set two groups that define a vector along which a biasing potential 
is applied. The net displacement of either of those groups (or any other 
atoms in the system) is a function of the total force acting on all of 
the atoms. Newtonian mechanics always apply, but it's not as simple as 
"pull on X, and Y moves." Your system evolves under the influence of the 
biasing force.


Your results are probably somewhat confounded by the fact that you're 
pulling along a vector that is oblique to both the helical axis and the 
hydrogen-bonding plane. It's not trivial to apply forces to duplex DNA, 
so judicious choice of pulling vector is critical.


-Justin



On Fri, Sep 14, 2018 at 5:11 PM, Justin Lemkul  wrote:



On 9/14/18 3:14 AM, Rakesh Mishra wrote:


Dear Dr. Justin,

Of course I agree with your points. There is no point to not believe on
you,
that's why we are discussing and thanks for your comment.
I raised the question because I observed the problem .
And it was matter of just common sense for me that
why the change of saving frequency is affecting the much difference
in the maximum value of force curve in pulling along the axial direction.

Let me clear again, I say Input parameters of the pull.mdp files are same
for both the simulation.
Only difference is the different saving frequency of position and energy
coordinates.
Please see below two cases

Case -A

simulation of same system with same input parameter during pulling
1  nstxtcout= 2000   ; every 4 ps
  nstenergy= 5000

2  nstxtcout= 2000   ; every 4 ps
  nstenergy= 2000

 (output files, pullf1.xvg, and pullf2.xvg are different very much
w.r.t
peak value of force )
  Same thing happening also in the following below case, please see
this.

Case B.

1  nstxtcout= 2000   ; every 4 ps
  nstenergy   = 5000

2-  nstxtcout= 1000   ; every 4 ps
   nstenergy   = 5000

Because, now this gromacs discussion user platform do not allow to upload
any other data (eg, plot, pdf file etc) otherwise I can upload the plot.


You can always upload images to file-sharing services and provide links.

But first, watch the trajectories and see how they're behaving. The
systems are likely just doing somewhat different things, as I said before.
There is no reason to expect even the exact same .tpr file to produce the
exact same output (binary identical), for reasons stated here:
http://www.gromacs.org/Documentation/Terminology/Reproducibility

Again, I emphasize that output control has no impact on the computation of
forces or anything to do with the pull code. This cannot be the reason for
differences in trajectories.

-Justin

On Thu, Sep 13, 2018 at 4:57 PM, Justin Lemkul  wrote:



On 9/13/18 1:20 AM, Rakesh Mishra wrote:

I do not believe .

Because if I run multiple simulation of pulling with the same system and
with the
same inputs then almost we are getting similar force/time curve.
While we are getting different curve if we are saving position
coordinates
or energy
coordinates with different frequency.

There is no aspect of the code in which the computation of forces

depends
on output frequency. You're welcome to disbelieve me, but you're clearly
just getting different simulation outcomes from different inputs, or
there's something else that differs that you haven't realized or haven't
told us.

-Justin


On Wed, Sep 12, 2018 at 8:15 PM, Justin Lemkul  wrote:


On 9/12/18 8:42 AM, Rakesh Mishra wrote:

Dear Justin


It is totally surprised for me.
 I am pulling the same system of bdna
with the same constant velocity (0.005nm/ps).

Case 1
let for first case, When I am saving position coordinate (nstxtc ) in
the
interval of 4ps
and saving energy coordinate in the interval of 4ps.

Case 2
In the second case of pulling of the same system with the same
velocity,
we
save position
coordinate in the interval of 4ps but we save energy coordinate in the
interval of  10ps.

Now in the output file of force.xvg for both case qualitative
behaviour
of
diagram is same but
Peak of the forces are much differ.  Why this saving frequency is
affecting
the peak value. While
it is just saving the coordinates.

We also found that, if we save energy coordinate with the same
frequency
and position
coordinate with different frequency then, again peak value of forces
are
different.
Which should not. Why it is happening. Can you clarify please.

Your results have nothing to do with the save frequency. The output in


pullf.xvg is specified by pull-nstfout, not any of the 

Re: [gmx-users] Justin paper 2010 pulling

[Rakesh Mishra]

Agreed.

But, I could not solve.
 So Justin, If I pull 3' end of one strand of DNA by taking as
3' end of the complimentary strand as a reference group (Note that
I have not fixed or not made it immobile ) then according to the theory of
newtons third law reference group (which is not immobile or not fixed )
will get
same equal and opposite pull and will move in the opposite direction.
am I correct.


On Fri, Sep 14, 2018 at 5:11 PM, Justin Lemkul  wrote:

>
>
> On 9/14/18 3:14 AM, Rakesh Mishra wrote:
>
>> Dear Dr. Justin,
>>
>> Of course I agree with your points. There is no point to not believe on
>> you,
>> that's why we are discussing and thanks for your comment.
>> I raised the question because I observed the problem .
>> And it was matter of just common sense for me that
>> why the change of saving frequency is affecting the much difference
>> in the maximum value of force curve in pulling along the axial direction.
>>
>> Let me clear again, I say Input parameters of the pull.mdp files are same
>> for both the simulation.
>> Only difference is the different saving frequency of position and energy
>> coordinates.
>> Please see below two cases
>>
>> Case -A
>>
>>simulation of same system with same input parameter during pulling
>> 1  nstxtcout= 2000   ; every 4 ps
>>  nstenergy= 5000
>>
>> 2  nstxtcout= 2000   ; every 4 ps
>>  nstenergy= 2000
>>
>> (output files, pullf1.xvg, and pullf2.xvg are different very much
>> w.r.t
>> peak value of force )
>>  Same thing happening also in the following below case, please see
>> this.
>>
>> Case B.
>>
>> 1  nstxtcout= 2000   ; every 4 ps
>>  nstenergy   = 5000
>>
>> 2-  nstxtcout= 1000   ; every 4 ps
>>   nstenergy   = 5000
>>
>> Because, now this gromacs discussion user platform do not allow to upload
>> any other data (eg, plot, pdf file etc) otherwise I can upload the plot.
>>
>
> You can always upload images to file-sharing services and provide links.
>
> But first, watch the trajectories and see how they're behaving. The
> systems are likely just doing somewhat different things, as I said before.
> There is no reason to expect even the exact same .tpr file to produce the
> exact same output (binary identical), for reasons stated here:
> http://www.gromacs.org/Documentation/Terminology/Reproducibility
>
> Again, I emphasize that output control has no impact on the computation of
> forces or anything to do with the pull code. This cannot be the reason for
> differences in trajectories.
>
> -Justin
>
> On Thu, Sep 13, 2018 at 4:57 PM, Justin Lemkul  wrote:
>>
>>
>>> On 9/13/18 1:20 AM, Rakesh Mishra wrote:
>>>
>>> I do not believe .

 Because if I run multiple simulation of pulling with the same system and
 with the
 same inputs then almost we are getting similar force/time curve.
 While we are getting different curve if we are saving position
 coordinates
 or energy
 coordinates with different frequency.

 There is no aspect of the code in which the computation of forces
>>> depends
>>> on output frequency. You're welcome to disbelieve me, but you're clearly
>>> just getting different simulation outcomes from different inputs, or
>>> there's something else that differs that you haven't realized or haven't
>>> told us.
>>>
>>> -Justin
>>>
>>>
>>> On Wed, Sep 12, 2018 at 8:15 PM, Justin Lemkul  wrote:
>>>

 On 9/12/18 8:42 AM, Rakesh Mishra wrote:
>
> Dear Justin
>
>> It is totally surprised for me.
>> I am pulling the same system of bdna
>> with the same constant velocity (0.005nm/ps).
>>
>> Case 1
>> let for first case, When I am saving position coordinate (nstxtc ) in
>> the
>> interval of 4ps
>> and saving energy coordinate in the interval of 4ps.
>>
>> Case 2
>> In the second case of pulling of the same system with the same
>> velocity,
>> we
>> save position
>> coordinate in the interval of 4ps but we save energy coordinate in the
>> interval of  10ps.
>>
>> Now in the output file of force.xvg for both case qualitative
>> behaviour
>> of
>> diagram is same but
>> Peak of the forces are much differ.  Why this saving frequency is
>> affecting
>> the peak value. While
>> it is just saving the coordinates.
>>
>> We also found that, if we save energy coordinate with the same
>> frequency
>> and position
>> coordinate with different frequency then, again peak value of forces
>> are
>> different.
>> Which should not. Why it is happening. Can you clarify please.
>>
>> Your results have nothing to do with the save frequency. The output in
>>
> pullf.xvg is specified by pull-nstfout, not any of the others. You have
> different simulations that behave differently, because there are
> elements
> of randomness in any MD simulation. Pulling is a non-equilibrium
> process;

Re: [gmx-users] Justin paper 2010 pulling

[Justin Lemkul]

On 9/14/18 3:14 AM, Rakesh Mishra wrote:

Dear Dr. Justin,

Of course I agree with your points. There is no point to not believe on you,
that's why we are discussing and thanks for your comment.
I raised the question because I observed the problem .
And it was matter of just common sense for me that
why the change of saving frequency is affecting the much difference
in the maximum value of force curve in pulling along the axial direction.

Let me clear again, I say Input parameters of the pull.mdp files are same
for both the simulation.
Only difference is the different saving frequency of position and energy
coordinates.
Please see below two cases

Case -A

   simulation of same system with same input parameter during pulling
1  nstxtcout= 2000   ; every 4 ps
 nstenergy= 5000

2  nstxtcout= 2000   ; every 4 ps
 nstenergy= 2000

(output files, pullf1.xvg, and pullf2.xvg are different very much w.r.t
peak value of force )
 Same thing happening also in the following below case, please see
this.

Case B.

1  nstxtcout= 2000   ; every 4 ps
 nstenergy   = 5000

2-  nstxtcout= 1000   ; every 4 ps
  nstenergy   = 5000

Because, now this gromacs discussion user platform do not allow to upload
any other data (eg, plot, pdf file etc) otherwise I can upload the plot.


You can always upload images to file-sharing services and provide links.

But first, watch the trajectories and see how they're behaving. The 
systems are likely just doing somewhat different things, as I said 
before. There is no reason to expect even the exact same .tpr file to 
produce the exact same output (binary identical), for reasons stated 
here: http://www.gromacs.org/Documentation/Terminology/Reproducibility


Again, I emphasize that output control has no impact on the computation 
of forces or anything to do with the pull code. This cannot be the 
reason for differences in trajectories.


-Justin


On Thu, Sep 13, 2018 at 4:57 PM, Justin Lemkul  wrote:



On 9/13/18 1:20 AM, Rakesh Mishra wrote:


I do not believe .

Because if I run multiple simulation of pulling with the same system and
with the
same inputs then almost we are getting similar force/time curve.
While we are getting different curve if we are saving position coordinates
or energy
coordinates with different frequency.


There is no aspect of the code in which the computation of forces depends
on output frequency. You're welcome to disbelieve me, but you're clearly
just getting different simulation outcomes from different inputs, or
there's something else that differs that you haven't realized or haven't
told us.

-Justin


On Wed, Sep 12, 2018 at 8:15 PM, Justin Lemkul  wrote:



On 9/12/18 8:42 AM, Rakesh Mishra wrote:

Dear Justin

It is totally surprised for me.
I am pulling the same system of bdna
with the same constant velocity (0.005nm/ps).

Case 1
let for first case, When I am saving position coordinate (nstxtc ) in
the
interval of 4ps
and saving energy coordinate in the interval of 4ps.

Case 2
In the second case of pulling of the same system with the same velocity,
we
save position
coordinate in the interval of 4ps but we save energy coordinate in the
interval of  10ps.

Now in the output file of force.xvg for both case qualitative behaviour
of
diagram is same but
Peak of the forces are much differ.  Why this saving frequency is
affecting
the peak value. While
it is just saving the coordinates.

We also found that, if we save energy coordinate with the same frequency
and position
coordinate with different frequency then, again peak value of forces are
different.
Which should not. Why it is happening. Can you clarify please.

Your results have nothing to do with the save frequency. The output in

pullf.xvg is specified by pull-nstfout, not any of the others. You have
different simulations that behave differently, because there are elements
of randomness in any MD simulation. Pulling is a non-equilibrium process;
you may have to run several times with different pull vectors to find the
minimum-energy path.

-Justin



On Thu, Sep 6, 2018 at 5:20 PM, Justin Lemkul  wrote:


On 9/6/18 2:29 AM, Rakesh Mishra wrote:

While I have purely physics background.


But, In my thinking, there are hydrogen bonds (electrostatic
attractive
interaction)
between bp of  both the strands of DNA/RNA  which are perpendicular to
helix direction.
And the other thing you have chosen very fast velocity like (0.01,
0.001,
0.005 ).
This can also be the reason of smoothness. But can you tell me one
thing
please,the
value of spring constant of biasing that you have taken (k= 1000), is
standard or not . If this value can be taken for peptide pulling .
Can
this value of
spring constant (k=1000) can be taken  for DNA (or dna+drug) pulling
or
not .

There is no such thing as a "standard" force cons
tant
for pulling.


-Justin

--

Re: [gmx-users] Justin paper 2010 pulling

[Rakesh Mishra]

Dear Dr. Justin,

Of course I agree with your points. There is no point to not believe on you,
that's why we are discussing and thanks for your comment.
I raised the question because I observed the problem .
And it was matter of just common sense for me that
why the change of saving frequency is affecting the much difference
in the maximum value of force curve in pulling along the axial direction.

Let me clear again, I say Input parameters of the pull.mdp files are same
for both the simulation.
Only difference is the different saving frequency of position and energy
coordinates.
Please see below two cases

Case -A

  simulation of same system with same input parameter during pulling
1  nstxtcout= 2000   ; every 4 ps
nstenergy= 5000

2  nstxtcout= 2000   ; every 4 ps
nstenergy= 2000

   (output files, pullf1.xvg, and pullf2.xvg are different very much w.r.t
peak value of force )
Same thing happening also in the following below case, please see
this.

Case B.

1  nstxtcout= 2000   ; every 4 ps
nstenergy   = 5000

2-  nstxtcout= 1000   ; every 4 ps
 nstenergy   = 5000

Because, now this gromacs discussion user platform do not allow to upload
any other data (eg, plot, pdf file etc) otherwise I can upload the plot.

On Thu, Sep 13, 2018 at 4:57 PM, Justin Lemkul  wrote:

>
>
> On 9/13/18 1:20 AM, Rakesh Mishra wrote:
>
>> I do not believe .
>>
>> Because if I run multiple simulation of pulling with the same system and
>> with the
>> same inputs then almost we are getting similar force/time curve.
>> While we are getting different curve if we are saving position coordinates
>> or energy
>> coordinates with different frequency.
>>
>
> There is no aspect of the code in which the computation of forces depends
> on output frequency. You're welcome to disbelieve me, but you're clearly
> just getting different simulation outcomes from different inputs, or
> there's something else that differs that you haven't realized or haven't
> told us.
>
> -Justin
>
>
> On Wed, Sep 12, 2018 at 8:15 PM, Justin Lemkul  wrote:
>>
>>
>>> On 9/12/18 8:42 AM, Rakesh Mishra wrote:
>>>
>>> Dear Justin

 It is totally surprised for me.
I am pulling the same system of bdna
 with the same constant velocity (0.005nm/ps).

 Case 1
 let for first case, When I am saving position coordinate (nstxtc ) in
 the
 interval of 4ps
 and saving energy coordinate in the interval of 4ps.

 Case 2
 In the second case of pulling of the same system with the same velocity,
 we
 save position
 coordinate in the interval of 4ps but we save energy coordinate in the
 interval of  10ps.

 Now in the output file of force.xvg for both case qualitative behaviour
 of
 diagram is same but
 Peak of the forces are much differ.  Why this saving frequency is
 affecting
 the peak value. While
 it is just saving the coordinates.

 We also found that, if we save energy coordinate with the same frequency
 and position
 coordinate with different frequency then, again peak value of forces are
 different.
 Which should not. Why it is happening. Can you clarify please.

 Your results have nothing to do with the save frequency. The output in
>>> pullf.xvg is specified by pull-nstfout, not any of the others. You have
>>> different simulations that behave differently, because there are elements
>>> of randomness in any MD simulation. Pulling is a non-equilibrium process;
>>> you may have to run several times with different pull vectors to find the
>>> minimum-energy path.
>>>
>>> -Justin
>>>
>>>
>>>
>>> On Thu, Sep 6, 2018 at 5:20 PM, Justin Lemkul  wrote:


 On 9/6/18 2:29 AM, Rakesh Mishra wrote:
>
> While I have purely physics background.
>
>> But, In my thinking, there are hydrogen bonds (electrostatic
>> attractive
>> interaction)
>> between bp of  both the strands of DNA/RNA  which are perpendicular to
>> helix direction.
>> And the other thing you have chosen very fast velocity like (0.01,
>> 0.001,
>> 0.005 ).
>> This can also be the reason of smoothness. But can you tell me one
>> thing
>> please,the
>> value of spring constant of biasing that you have taken (k= 1000), is
>> standard or not . If this value can be taken for peptide pulling .
>> Can
>> this value of
>> spring constant (k=1000) can be taken  for DNA (or dna+drug) pulling
>> or
>> not .
>>
>> There is no such thing as a "standard" force cons
>> tant
>> for pulling.
>>
> -Justin
>
> --
> ==
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
> 340 West Campus Dr.
> 

Re: [gmx-users] Justin paper 2010 pulling

[Justin Lemkul]

On 9/13/18 1:20 AM, Rakesh Mishra wrote:

I do not believe .

Because if I run multiple simulation of pulling with the same system and
with the
same inputs then almost we are getting similar force/time curve.
While we are getting different curve if we are saving position coordinates
or energy
coordinates with different frequency.


There is no aspect of the code in which the computation of forces 
depends on output frequency. You're welcome to disbelieve me, but you're 
clearly just getting different simulation outcomes from different 
inputs, or there's something else that differs that you haven't realized 
or haven't told us.


-Justin


On Wed, Sep 12, 2018 at 8:15 PM, Justin Lemkul  wrote:



On 9/12/18 8:42 AM, Rakesh Mishra wrote:


Dear Justin

It is totally surprised for me.
   I am pulling the same system of bdna
with the same constant velocity (0.005nm/ps).

Case 1
let for first case, When I am saving position coordinate (nstxtc ) in the
interval of 4ps
and saving energy coordinate in the interval of 4ps.

Case 2
In the second case of pulling of the same system with the same velocity,
we
save position
coordinate in the interval of 4ps but we save energy coordinate in the
interval of  10ps.

Now in the output file of force.xvg for both case qualitative behaviour of
diagram is same but
Peak of the forces are much differ.  Why this saving frequency is
affecting
the peak value. While
it is just saving the coordinates.

We also found that, if we save energy coordinate with the same frequency
and position
coordinate with different frequency then, again peak value of forces are
different.
Which should not. Why it is happening. Can you clarify please.


Your results have nothing to do with the save frequency. The output in
pullf.xvg is specified by pull-nstfout, not any of the others. You have
different simulations that behave differently, because there are elements
of randomness in any MD simulation. Pulling is a non-equilibrium process;
you may have to run several times with different pull vectors to find the
minimum-energy path.

-Justin




On Thu, Sep 6, 2018 at 5:20 PM, Justin Lemkul  wrote:



On 9/6/18 2:29 AM, Rakesh Mishra wrote:

While I have purely physics background.

But, In my thinking, there are hydrogen bonds (electrostatic attractive
interaction)
between bp of  both the strands of DNA/RNA  which are perpendicular to
helix direction.
And the other thing you have chosen very fast velocity like (0.01,
0.001,
0.005 ).
This can also be the reason of smoothness. But can you tell me one thing
please,the
value of spring constant of biasing that you have taken (k= 1000), is
standard or not . If this value can be taken for peptide pulling .  Can
this value of
spring constant (k=1000) can be taken  for DNA (or dna+drug) pulling or
not .

There is no such thing as a "standard" force constant for pulling.

-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.thelemkullab.com

==

--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support
/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

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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.thelemkullab.com

==

--
Gromacs Users mailing list

* Please search the archive at http://www.gromacs.org/Support
/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* 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.thelemkullab.com

==

--
Gromacs Users mailing list

* Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!

* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

* 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.

Re: [gmx-users] Justin paper 2010 pulling

[Rakesh Mishra]

I do not believe .

Because if I run multiple simulation of pulling with the same system and
with the
same inputs then almost we are getting similar force/time curve.
While we are getting different curve if we are saving position coordinates
or energy
coordinates with different frequency.

On Wed, Sep 12, 2018 at 8:15 PM, Justin Lemkul  wrote:

>
>
> On 9/12/18 8:42 AM, Rakesh Mishra wrote:
>
>> Dear Justin
>>
>> It is totally surprised for me.
>>   I am pulling the same system of bdna
>> with the same constant velocity (0.005nm/ps).
>>
>> Case 1
>> let for first case, When I am saving position coordinate (nstxtc ) in the
>> interval of 4ps
>> and saving energy coordinate in the interval of 4ps.
>>
>> Case 2
>> In the second case of pulling of the same system with the same velocity,
>> we
>> save position
>> coordinate in the interval of 4ps but we save energy coordinate in the
>> interval of  10ps.
>>
>> Now in the output file of force.xvg for both case qualitative behaviour of
>> diagram is same but
>> Peak of the forces are much differ.  Why this saving frequency is
>> affecting
>> the peak value. While
>> it is just saving the coordinates.
>>
>> We also found that, if we save energy coordinate with the same frequency
>> and position
>> coordinate with different frequency then, again peak value of forces are
>> different.
>> Which should not. Why it is happening. Can you clarify please.
>>
>
> Your results have nothing to do with the save frequency. The output in
> pullf.xvg is specified by pull-nstfout, not any of the others. You have
> different simulations that behave differently, because there are elements
> of randomness in any MD simulation. Pulling is a non-equilibrium process;
> you may have to run several times with different pull vectors to find the
> minimum-energy path.
>
> -Justin
>
>
>
>> On Thu, Sep 6, 2018 at 5:20 PM, Justin Lemkul  wrote:
>>
>>
>>> On 9/6/18 2:29 AM, Rakesh Mishra wrote:
>>>
>>> While I have purely physics background.

 But, In my thinking, there are hydrogen bonds (electrostatic attractive
 interaction)
 between bp of  both the strands of DNA/RNA  which are perpendicular to
 helix direction.
 And the other thing you have chosen very fast velocity like (0.01,
 0.001,
 0.005 ).
 This can also be the reason of smoothness. But can you tell me one thing
 please,the
 value of spring constant of biasing that you have taken (k= 1000), is
 standard or not . If this value can be taken for peptide pulling .  Can
 this value of
 spring constant (k=1000) can be taken  for DNA (or dna+drug) pulling or
 not .

 There is no such thing as a "standard" force constant for pulling.
>>>
>>> -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.thelemkullab.com
>>>
>>> ==
>>>
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/Support
>>> /Mailing_Lists/GMX-Users_List before posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * 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.thelemkullab.com
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * 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.
>



-- 

*With Best-Rakesh Kumar Mishra*
*  (RA)CSD  SINP Kolkata, India*

*E-mail - rakesh.mis...@saha.ac.in  *

*Phone n. +91 9473662491, +918777496532*
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Re: [gmx-users] Justin paper 2010 pulling

[Justin Lemkul]

On 9/12/18 8:42 AM, Rakesh Mishra wrote:

Dear Justin

It is totally surprised for me.
  I am pulling the same system of bdna
with the same constant velocity (0.005nm/ps).

Case 1
let for first case, When I am saving position coordinate (nstxtc ) in the
interval of 4ps
and saving energy coordinate in the interval of 4ps.

Case 2
In the second case of pulling of the same system with the same velocity, we
save position
coordinate in the interval of 4ps but we save energy coordinate in the
interval of  10ps.

Now in the output file of force.xvg for both case qualitative behaviour of
diagram is same but
Peak of the forces are much differ.  Why this saving frequency is affecting
the peak value. While
it is just saving the coordinates.

We also found that, if we save energy coordinate with the same frequency
and position
coordinate with different frequency then, again peak value of forces are
different.
Which should not. Why it is happening. Can you clarify please.


Your results have nothing to do with the save frequency. The output in 
pullf.xvg is specified by pull-nstfout, not any of the others. You have 
different simulations that behave differently, because there are 
elements of randomness in any MD simulation. Pulling is a 
non-equilibrium process; you may have to run several times with 
different pull vectors to find the minimum-energy path.


-Justin



On Thu, Sep 6, 2018 at 5:20 PM, Justin Lemkul  wrote:



On 9/6/18 2:29 AM, Rakesh Mishra wrote:


While I have purely physics background.

But, In my thinking, there are hydrogen bonds (electrostatic attractive
interaction)
between bp of  both the strands of DNA/RNA  which are perpendicular to
helix direction.
And the other thing you have chosen very fast velocity like (0.01, 0.001,
0.005 ).
This can also be the reason of smoothness. But can you tell me one thing
please,the
value of spring constant of biasing that you have taken (k= 1000), is
standard or not . If this value can be taken for peptide pulling .  Can
this value of
spring constant (k=1000) can be taken  for DNA (or dna+drug) pulling or
not .


There is no such thing as a "standard" force constant for pulling.

-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.thelemkullab.com

==

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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.thelemkullab.com

==

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Re: [gmx-users] Justin paper 2010 pulling

[Adrian Devitt-Lee]

What do you mean by "different" peak forces?

Have you run multiple simulations with the same settings to see how much
your peak force varies? It may be that the force just has a high variance.

Best,
Adrian Devitt-Lee

On Wed, Sep 12, 2018 at 1:44 PM Rakesh Mishra  wrote:

> Dear Justin
>
> It is totally surprised for me.
>  I am pulling the same system of bdna
> with the same constant velocity (0.005nm/ps).
>
> Case 1
> let for first case, When I am saving position coordinate (nstxtc ) in the
> interval of 4ps
> and saving energy coordinate in the interval of 4ps.
>
> Case 2
> In the second case of pulling of the same system with the same velocity, we
> save position
> coordinate in the interval of 4ps but we save energy coordinate in the
> interval of  10ps.
>
> Now in the output file of force.xvg for both case qualitative behaviour of
> diagram is same but
> Peak of the forces are much differ.  Why this saving frequency is affecting
> the peak value. While
> it is just saving the coordinates.
>
> We also found that, if we save energy coordinate with the same frequency
> and position
> coordinate with different frequency then, again peak value of forces are
> different.
> Which should not. Why it is happening. Can you clarify please.
>
>
> On Thu, Sep 6, 2018 at 5:20 PM, Justin Lemkul  wrote:
>
> >
> >
> > On 9/6/18 2:29 AM, Rakesh Mishra wrote:
> >
> >> While I have purely physics background.
> >>
> >> But, In my thinking, there are hydrogen bonds (electrostatic attractive
> >> interaction)
> >> between bp of  both the strands of DNA/RNA  which are perpendicular to
> >> helix direction.
> >> And the other thing you have chosen very fast velocity like (0.01,
> 0.001,
> >> 0.005 ).
> >> This can also be the reason of smoothness. But can you tell me one thing
> >> please,the
> >> value of spring constant of biasing that you have taken (k= 1000), is
> >> standard or not . If this value can be taken for peptide pulling .  Can
> >> this value of
> >> spring constant (k=1000) can be taken  for DNA (or dna+drug) pulling or
> >> not .
> >>
> >
> > There is no such thing as a "standard" force constant for pulling.
> >
> > -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.thelemkullab.com
> >
> > ==
> >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/Support
> > /Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * 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.
> >
>
>
>
> --
>
> *With Best-Rakesh Kumar Mishra*
> *  (RA)CSD  SINP Kolkata, India*
>
> *E-mail - rakesh.mis...@saha.ac.in  *
>
> *Phone n. +91 9473662491, +918777496532*
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
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>
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> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-requ...@gromacs.org.
>
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Re: [gmx-users] Justin paper 2010 pulling

[Rakesh Mishra]

Dear Justin

It is totally surprised for me.
 I am pulling the same system of bdna
with the same constant velocity (0.005nm/ps).

Case 1
let for first case, When I am saving position coordinate (nstxtc ) in the
interval of 4ps
and saving energy coordinate in the interval of 4ps.

Case 2
In the second case of pulling of the same system with the same velocity, we
save position
coordinate in the interval of 4ps but we save energy coordinate in the
interval of  10ps.

Now in the output file of force.xvg for both case qualitative behaviour of
diagram is same but
Peak of the forces are much differ.  Why this saving frequency is affecting
the peak value. While
it is just saving the coordinates.

We also found that, if we save energy coordinate with the same frequency
and position
coordinate with different frequency then, again peak value of forces are
different.
Which should not. Why it is happening. Can you clarify please.


On Thu, Sep 6, 2018 at 5:20 PM, Justin Lemkul  wrote:

>
>
> On 9/6/18 2:29 AM, Rakesh Mishra wrote:
>
>> While I have purely physics background.
>>
>> But, In my thinking, there are hydrogen bonds (electrostatic attractive
>> interaction)
>> between bp of  both the strands of DNA/RNA  which are perpendicular to
>> helix direction.
>> And the other thing you have chosen very fast velocity like (0.01, 0.001,
>> 0.005 ).
>> This can also be the reason of smoothness. But can you tell me one thing
>> please,the
>> value of spring constant of biasing that you have taken (k= 1000), is
>> standard or not . If this value can be taken for peptide pulling .  Can
>> this value of
>> spring constant (k=1000) can be taken  for DNA (or dna+drug) pulling or
>> not .
>>
>
> There is no such thing as a "standard" force constant for pulling.
>
> -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.thelemkullab.com
>
> ==
>
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * 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.
>



-- 

*With Best-Rakesh Kumar Mishra*
*  (RA)CSD  SINP Kolkata, India*

*E-mail - rakesh.mis...@saha.ac.in  *

*Phone n. +91 9473662491, +918777496532*
-- 
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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Justin paper 2010 pulling

[Justin Lemkul]

On 9/6/18 2:29 AM, Rakesh Mishra wrote:

While I have purely physics background.

But, In my thinking, there are hydrogen bonds (electrostatic attractive
interaction)
between bp of  both the strands of DNA/RNA  which are perpendicular to
helix direction.
And the other thing you have chosen very fast velocity like (0.01, 0.001,
0.005 ).
This can also be the reason of smoothness. But can you tell me one thing
please,the
value of spring constant of biasing that you have taken (k= 1000), is
standard or not . If this value can be taken for peptide pulling .  Can
this value of
spring constant (k=1000) can be taken  for DNA (or dna+drug) pulling or
not .


There is no such thing as a "standard" force constant for pulling.

-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.thelemkullab.com

==

--
Gromacs Users mailing list

* Please search the archive at 
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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Justin paper 2010 pulling

[Rakesh Mishra]

While I have purely physics background.

But, In my thinking, there are hydrogen bonds (electrostatic attractive
interaction)
between bp of  both the strands of DNA/RNA  which are perpendicular to
helix direction.
And the other thing you have chosen very fast velocity like (0.01, 0.001,
0.005 ).
This can also be the reason of smoothness. But can you tell me one thing
please,the
value of spring constant of biasing that you have taken (k= 1000), is
standard or not . If this value can be taken for peptide pulling .  Can
this value of
spring constant (k=1000) can be taken  for DNA (or dna+drug) pulling or
not .




On Thu, Sep 6, 2018 at 5:31 AM, Justin Lemkul  wrote:

>
>
> On 9/5/18 1:50 AM, Rakesh Mishra wrote:
>
>> So that means
>>
>> It is may be due to the  difference in the type of interaction.
>>
>> and I can not understand your this statement "you have to contend with
>> forces principally acting perpendicular to the direction of the bias"
>>
>>
> Well, what interactions act along the plane perpendicular to the helix
> axis of a duplex DNA or RNA?
>
> -Justin
>
>
>
>> On Tue, Sep 4, 2018 at 10:54 PM, Justin Lemkul  wrote:
>>
>>
>>> On 9/4/18 11:44 AM, Rakesh Mishra wrote:
>>>
>>> Dear Justin,

 Seriously I want to remove my confusion.
 I just read your one paper " J.Physical Chemistry B 2010, 114, 1652-60"
 Where you have studied stability of Alzheimer. I don't want to ask about
 umbrella sampling used for the calculation of PMF.

 But , before the calculation of PMF , you
 have obtained simple dissociation using your  pulling protocol of
 gromacs
 with constant velocity simulation at three different velocities.  I am
 surprised that you have followed the obvious protocol
 of minimization the nvt the npt and then 100ns md production. then you
 took
 final structure of 100ns and made new box for pulling  and followed the
 same minimisation and npt for short time. After this you did pulling
 along
 only one direction (one reaction coordinate) .

 I am surprised that how such a smooth force/time data you have obtained
 for
 all the velocities (0.01,0.001,0.005) . I am asking because for my
 simple
 12bp dsDNA or 22bp siRNA , I also have followed similar protocol and
 fixed
 one end (say 5') of first strand and pulling opposite end (5') of second
 strand along the helical direction of the system. Here, I am getting
 force/time (in the .xvg ) data which is qualitatively similar behaviour
 like yours i.e.  initially increasing then reach to maximum and then
 decreasing almost becomes to zero value. But , In mine case during
 initial
 time of pulling force is also negative as well large fluctuation of
 force
 .
 But not such a smooth Variation of force/time like your in this paper.
 In
 your case, force is increasing like linearly in the initial and reaches
 the
 maximum and then start to decrease.  There is no problem to
 clarify the peak of force (maximum force) in your pulling (above
 mentioned
 paper). While in our case its very difficult to clarify the peak force
 due
 to large fluctuation in value.
 Can you please tell me something about the reason. Its smoothness is now
 became headache for my calculation in all the case of pulling.

 There is no reason to think that your outcome and mine should look
>>> anything alike. Pulling apart two proteins that interact in the way the
>>> peptides do in a protofibril is much simpler than the intertwined nature
>>> of
>>> a DNA or RNA duplex. If you pull along the helix axis, you have to
>>> contend
>>> with forces principally acting perpendicular to the direction of the
>>> bias,
>>> as well as the fact that the strands have to slide past one another,
>>> requiring major distortion of the helix and/or frictional forces due to
>>> the
>>> individual strands unwinding from one another.
>>>
>>> -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.thelemkullab.com
>>>
>>> ==
>>>
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/Support
>>> /Mailing_Lists/GMX-Users_List before posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * 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 

Re: [gmx-users] Justin paper 2010 pulling

[Justin Lemkul]

On 9/5/18 1:50 AM, Rakesh Mishra wrote:

So that means

It is may be due to the  difference in the type of interaction.

and I can not understand your this statement "you have to contend with
forces principally acting perpendicular to the direction of the bias"



Well, what interactions act along the plane perpendicular to the helix 
axis of a duplex DNA or RNA?


-Justin



On Tue, Sep 4, 2018 at 10:54 PM, Justin Lemkul  wrote:



On 9/4/18 11:44 AM, Rakesh Mishra wrote:


Dear Justin,

Seriously I want to remove my confusion.
I just read your one paper " J.Physical Chemistry B 2010, 114, 1652-60"
Where you have studied stability of Alzheimer. I don't want to ask about
umbrella sampling used for the calculation of PMF.

But , before the calculation of PMF , you
have obtained simple dissociation using your  pulling protocol of gromacs
with constant velocity simulation at three different velocities.  I am
surprised that you have followed the obvious protocol
of minimization the nvt the npt and then 100ns md production. then you
took
final structure of 100ns and made new box for pulling  and followed the
same minimisation and npt for short time. After this you did pulling along
only one direction (one reaction coordinate) .

I am surprised that how such a smooth force/time data you have obtained
for
all the velocities (0.01,0.001,0.005) . I am asking because for my simple
12bp dsDNA or 22bp siRNA , I also have followed similar protocol and fixed
one end (say 5') of first strand and pulling opposite end (5') of second
strand along the helical direction of the system. Here, I am getting
force/time (in the .xvg ) data which is qualitatively similar behaviour
like yours i.e.  initially increasing then reach to maximum and then
decreasing almost becomes to zero value. But , In mine case during initial
time of pulling force is also negative as well large fluctuation of force
.
But not such a smooth Variation of force/time like your in this paper. In
your case, force is increasing like linearly in the initial and reaches
the
maximum and then start to decrease.  There is no problem to
clarify the peak of force (maximum force) in your pulling (above mentioned
paper). While in our case its very difficult to clarify the peak force due
to large fluctuation in value.
Can you please tell me something about the reason. Its smoothness is now
became headache for my calculation in all the case of pulling.


There is no reason to think that your outcome and mine should look
anything alike. Pulling apart two proteins that interact in the way the
peptides do in a protofibril is much simpler than the intertwined nature of
a DNA or RNA duplex. If you pull along the helix axis, you have to contend
with forces principally acting perpendicular to the direction of the bias,
as well as the fact that the strands have to slide past one another,
requiring major distortion of the helix and/or frictional forces due to the
individual strands unwinding from one another.

-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.thelemkullab.com

==

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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.thelemkullab.com

==

--
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* Please search the archive at 
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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Justin paper 2010 pulling

[Rakesh Mishra]

So that means

It is may be due to the  difference in the type of interaction.

and I can not understand your this statement "you have to contend with
forces principally acting perpendicular to the direction of the bias"



On Tue, Sep 4, 2018 at 10:54 PM, Justin Lemkul  wrote:

>
>
> On 9/4/18 11:44 AM, Rakesh Mishra wrote:
>
>> Dear Justin,
>>
>> Seriously I want to remove my confusion.
>> I just read your one paper " J.Physical Chemistry B 2010, 114, 1652-60"
>> Where you have studied stability of Alzheimer. I don't want to ask about
>> umbrella sampling used for the calculation of PMF.
>>
>> But , before the calculation of PMF , you
>> have obtained simple dissociation using your  pulling protocol of gromacs
>> with constant velocity simulation at three different velocities.  I am
>> surprised that you have followed the obvious protocol
>> of minimization the nvt the npt and then 100ns md production. then you
>> took
>> final structure of 100ns and made new box for pulling  and followed the
>> same minimisation and npt for short time. After this you did pulling along
>> only one direction (one reaction coordinate) .
>>
>> I am surprised that how such a smooth force/time data you have obtained
>> for
>> all the velocities (0.01,0.001,0.005) . I am asking because for my simple
>> 12bp dsDNA or 22bp siRNA , I also have followed similar protocol and fixed
>> one end (say 5') of first strand and pulling opposite end (5') of second
>> strand along the helical direction of the system. Here, I am getting
>> force/time (in the .xvg ) data which is qualitatively similar behaviour
>> like yours i.e.  initially increasing then reach to maximum and then
>> decreasing almost becomes to zero value. But , In mine case during initial
>> time of pulling force is also negative as well large fluctuation of force
>> .
>> But not such a smooth Variation of force/time like your in this paper. In
>> your case, force is increasing like linearly in the initial and reaches
>> the
>> maximum and then start to decrease.  There is no problem to
>> clarify the peak of force (maximum force) in your pulling (above mentioned
>> paper). While in our case its very difficult to clarify the peak force due
>> to large fluctuation in value.
>> Can you please tell me something about the reason. Its smoothness is now
>> became headache for my calculation in all the case of pulling.
>>
>
> There is no reason to think that your outcome and mine should look
> anything alike. Pulling apart two proteins that interact in the way the
> peptides do in a protofibril is much simpler than the intertwined nature of
> a DNA or RNA duplex. If you pull along the helix axis, you have to contend
> with forces principally acting perpendicular to the direction of the bias,
> as well as the fact that the strands have to slide past one another,
> requiring major distortion of the helix and/or frictional forces due to the
> individual strands unwinding from one another.
>
> -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.thelemkullab.com
>
> ==
>
> --
> Gromacs Users mailing list
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*With Best-Rakesh Kumar Mishra*
*  (RA)CSD  SINP Kolkata, India*

*E-mail - rakesh.mis...@saha.ac.in  *

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Re: [gmx-users] Justin paper 2010 pulling

[Justin Lemkul]

On 9/4/18 11:44 AM, Rakesh Mishra wrote:

Dear Justin,

Seriously I want to remove my confusion.
I just read your one paper " J.Physical Chemistry B 2010, 114, 1652-60"
Where you have studied stability of Alzheimer. I don't want to ask about
umbrella sampling used for the calculation of PMF.

But , before the calculation of PMF , you
have obtained simple dissociation using your  pulling protocol of gromacs
with constant velocity simulation at three different velocities.  I am
surprised that you have followed the obvious protocol
of minimization the nvt the npt and then 100ns md production. then you took
final structure of 100ns and made new box for pulling  and followed the
same minimisation and npt for short time. After this you did pulling along
only one direction (one reaction coordinate) .

I am surprised that how such a smooth force/time data you have obtained for
all the velocities (0.01,0.001,0.005) . I am asking because for my simple
12bp dsDNA or 22bp siRNA , I also have followed similar protocol and fixed
one end (say 5') of first strand and pulling opposite end (5') of second
strand along the helical direction of the system. Here, I am getting
force/time (in the .xvg ) data which is qualitatively similar behaviour
like yours i.e.  initially increasing then reach to maximum and then
decreasing almost becomes to zero value. But , In mine case during initial
time of pulling force is also negative as well large fluctuation of force .
But not such a smooth Variation of force/time like your in this paper. In
your case, force is increasing like linearly in the initial and reaches the
maximum and then start to decrease.  There is no problem to
clarify the peak of force (maximum force) in your pulling (above mentioned
paper). While in our case its very difficult to clarify the peak force due
to large fluctuation in value.
Can you please tell me something about the reason. Its smoothness is now
became headache for my calculation in all the case of pulling.


There is no reason to think that your outcome and mine should look 
anything alike. Pulling apart two proteins that interact in the way the 
peptides do in a protofibril is much simpler than the intertwined nature 
of a DNA or RNA duplex. If you pull along the helix axis, you have to 
contend with forces principally acting perpendicular to the direction of 
the bias, as well as the fact that the strands have to slide past one 
another, requiring major distortion of the helix and/or frictional 
forces due to the individual strands unwinding from one another.


-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.thelemkullab.com

==

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