Re: [gmx-users] Pulling two groups in opposite direction

2018-05-18 Thread Justin Lemkul 



On 5/18/18 6:34 AM, Naba wrote:

On 5/17/18 1:39 AM, Naba wrote:

On 5/16/18 3:32 AM, Naba wrote:

Dear all,

I am using gromacs 5.1.2 and trying to pull both monomers of 128 amino
acids from its homodimer in opposite directions along z axis. The
interfaces of each protein chain is parallel to the z axis. I do not

need

any restraints in this case. I have gone through the GROMACS manual and
some of the previous archived messages and set the following mdp

options.

; Pull code
pull= yes
pull_ngroups= 2
pull_ncoords= 2
pull_group1_name= chain_A
pull_group2_name= chain_B
;pull_group3_name = Protein
pull_coord1_type = umbrella
pull_coord2_type = umbrella
pull_coord1_init = 0.0
pull_coord2_init = 0.0
pull_coord1_start = yes   ; define initial COM distance > 0
pull_coord2_start = yes
pull_coord1_geometry= direction
pull_coord2_geometry= direction
pull_coord1_groups  = 2 1
pull_coord2_groups  = 1 2
pull_coord1_dim = N N Y
pull_coord2_dim = N N Y

Note that pull_coord*_dim is not relevant when using "direction"

geometry.

pull_coord1_rate= 0.01; 0.008 nm per ps = 8 nm per ns
pull_coord2_rate= 0.01 ; 0.008 nm per ps = 8 nm per ns
pull_coord1_k   = 2000  ; kJ mol^-1 nm^-2
pull_coord2_k   = 2000
pull_coord1_vec= 0.0 0.0 1.0
pull_coord2_vec= 0.0 0.0 -1.0
nstcalcenergy = 1
nhchainlength = 1

But it fails to pull chain_A in positive z direction. However, chain_B

is

seemed to pull in negative z direction. Someone please suggest the

proper

way to pull two groups in opposite directions, or if there is anything

that

I am missing.

What is the point of pulling in two directions? Separation of two
species requires only one reaction coordinate. For every action, there
is an equal, but opposite reaction...

-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

==


Thank you Dr. Justin.
Besides PMF calculations during umbrella sampling, I want to observe the
interacting residues while pulling both the chain in opposite directions.
In your tutorial you pulled only one chain for your specific case.

Whereas

in my case, the point to be observed how smoothly or rigorously the

chains

are interacting with their residues in interface due to the application

of

two equal forces in opposite directions.

Anyways, from your reply should I understand that pulling only one chain
without any restraints in only one direction will do my job? Please

correct

me the mdp settings.

Do not pull along only one dimension. A normal, soluble protein complex
will rotate in space so you should pull in all three dimensions. There
are several ways to accomplish this pulling, but indeed you only need
one reaction coordinate to induce separation.

-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

==

Thank you again Dr. Justin.

How do I pull only chain so that both the chains should show sliding
movement  with respect to one another?

For your convenience here is the picture of the homodimer I am dealing
with: https://www.dropbox.com/s/6yh5vo3jcieh7rm/dummy.png?dl=0 . I want to
pull the chains in the direction with the arrow marks given there in the
picture.

More precisely, it is N-terminal part of a very huge insoluble protein
reported to be in dimeric form. However, comm-mode = Linear showed me
unexpected rotation at very beginning of the run which entirely disturbed
the initial orientation of the molecule along z axis. In contrast,
comm-mode = Angular and pull_coord1_dim = Y Y Y with pull_ncoords = 1
partially fulfilled my purpose but not in that way as I want both chains to
be slide over one another.

Hope you will make me more clear about all these.


For a periodic system, comm-mode = angular does not make sense.

If you want a simple sliding motion, then try pulling along only one axis.

-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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Re: [gmx-users] Pulling two groups in opposite direction

2018-05-18 Thread Naba 
>
> On 5/17/18 1:39 AM, Naba wrote:
> >> On 5/16/18 3:32 AM, Naba wrote:
> >>> Dear all,
> >>>
> >>> I am using gromacs 5.1.2 and trying to pull both monomers of 128 amino
> >>> acids from its homodimer in opposite directions along z axis. The
> >>> interfaces of each protein chain is parallel to the z axis. I do not
> need
> >>> any restraints in this case. I have gone through the GROMACS manual and
> >>> some of the previous archived messages and set the following mdp
> options.
> >>>
> >>> ; Pull code
> >>> pull= yes
> >>> pull_ngroups= 2
> >>> pull_ncoords= 2
> >>> pull_group1_name= chain_A
> >>> pull_group2_name= chain_B
> >>> ;pull_group3_name = Protein
> >>> pull_coord1_type = umbrella
> >>> pull_coord2_type = umbrella
> >>> pull_coord1_init = 0.0
> >>> pull_coord2_init = 0.0
> >>> pull_coord1_start = yes   ; define initial COM distance > 0
> >>> pull_coord2_start = yes
> >>> pull_coord1_geometry= direction
> >>> pull_coord2_geometry= direction
> >>> pull_coord1_groups  = 2 1
> >>> pull_coord2_groups  = 1 2
> >>> pull_coord1_dim = N N Y
> >>> pull_coord2_dim = N N Y
> >> Note that pull_coord*_dim is not relevant when using "direction"
> geometry.
> >>
> >>> pull_coord1_rate= 0.01; 0.008 nm per ps = 8 nm per ns
> >>> pull_coord2_rate= 0.01 ; 0.008 nm per ps = 8 nm per ns
> >>> pull_coord1_k   = 2000  ; kJ mol^-1 nm^-2
> >>> pull_coord2_k   = 2000
> >>> pull_coord1_vec= 0.0 0.0 1.0
> >>> pull_coord2_vec= 0.0 0.0 -1.0
> >>> nstcalcenergy = 1
> >>> nhchainlength = 1
> >>>
> >>> But it fails to pull chain_A in positive z direction. However, chain_B
> is
> >>> seemed to pull in negative z direction. Someone please suggest the
> proper
> >>> way to pull two groups in opposite directions, or if there is anything
> >> that
> >>> I am missing.
> >> What is the point of pulling in two directions? Separation of two
> >> species requires only one reaction coordinate. For every action, there
> >> is an equal, but opposite reaction...
> >>
> >> -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
> >>
> >> ==
> >
> >
> > Thank you Dr. Justin.
> > Besides PMF calculations during umbrella sampling, I want to observe the
> > interacting residues while pulling both the chain in opposite directions.
> > In your tutorial you pulled only one chain for your specific case.
> Whereas
> > in my case, the point to be observed how smoothly or rigorously the
> chains
> > are interacting with their residues in interface due to the application
> of
> > two equal forces in opposite directions.
> >
> > Anyways, from your reply should I understand that pulling only one chain
> > without any restraints in only one direction will do my job? Please
> correct
> > me the mdp settings.
>
> Do not pull along only one dimension. A normal, soluble protein complex
> will rotate in space so you should pull in all three dimensions. There
> are several ways to accomplish this pulling, but indeed you only need
> one reaction coordinate to induce separation.
>
> -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
>
> ==
>
> Thank you again Dr. Justin.

How do I pull only chain so that both the chains should show sliding
movement  with respect to one another?

For your convenience here is the picture of the homodimer I am dealing
with: https://www.dropbox.com/s/6yh5vo3jcieh7rm/dummy.png?dl=0 . I want to
pull the chains in the direction with the arrow marks given there in the
picture.

More precisely, it is N-terminal part of a very huge insoluble protein
reported to be in dimeric form. However, comm-mode = Linear showed me
unexpected rotation at very beginning of the run which entirely disturbed
the initial orientation of the molecule along z axis. In contrast,
comm-mode = Angular and pull_coord1_dim = Y Y Y with pull_ncoords = 1
partially fulfilled my purpose but not in that way as I want both chains to
be slide over one another.

Hope you will make me more clear about all these.


Nabajyoti Goswami

Research Associate
Bioinformatics Infrastructure Facility
Department of Animal Biotechnology
College of Veterinary Science
Khanapara,Guwahati 781022
Assam, India
-- 
Gromacs Users mailing list

* Please search the archive at

Re: [gmx-users] Pulling two groups in opposite direction

2018-05-17 Thread Justin Lemkul 



On 5/17/18 1:39 AM, Naba wrote:

On 5/16/18 3:32 AM, Naba wrote:

Dear all,

I am using gromacs 5.1.2 and trying to pull both monomers of 128 amino
acids from its homodimer in opposite directions along z axis. The
interfaces of each protein chain is parallel to the z axis. I do not need
any restraints in this case. I have gone through the GROMACS manual and
some of the previous archived messages and set the following mdp options.

; Pull code
pull= yes
pull_ngroups= 2
pull_ncoords= 2
pull_group1_name= chain_A
pull_group2_name= chain_B
;pull_group3_name = Protein
pull_coord1_type = umbrella
pull_coord2_type = umbrella
pull_coord1_init = 0.0
pull_coord2_init = 0.0
pull_coord1_start = yes   ; define initial COM distance > 0
pull_coord2_start = yes
pull_coord1_geometry= direction
pull_coord2_geometry= direction
pull_coord1_groups  = 2 1
pull_coord2_groups  = 1 2
pull_coord1_dim = N N Y
pull_coord2_dim = N N Y

Note that pull_coord*_dim is not relevant when using "direction" geometry.


pull_coord1_rate= 0.01; 0.008 nm per ps = 8 nm per ns
pull_coord2_rate= 0.01 ; 0.008 nm per ps = 8 nm per ns
pull_coord1_k   = 2000  ; kJ mol^-1 nm^-2
pull_coord2_k   = 2000
pull_coord1_vec= 0.0 0.0 1.0
pull_coord2_vec= 0.0 0.0 -1.0
nstcalcenergy = 1
nhchainlength = 1

But it fails to pull chain_A in positive z direction. However, chain_B is
seemed to pull in negative z direction. Someone please suggest the proper
way to pull two groups in opposite directions, or if there is anything

that

I am missing.

What is the point of pulling in two directions? Separation of two
species requires only one reaction coordinate. For every action, there
is an equal, but opposite reaction...

-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

==



Thank you Dr. Justin.
Besides PMF calculations during umbrella sampling, I want to observe the
interacting residues while pulling both the chain in opposite directions.
In your tutorial you pulled only one chain for your specific case. Whereas
in my case, the point to be observed how smoothly or rigorously the chains
are interacting with their residues in interface due to the application of
two equal forces in opposite directions.

Anyways, from your reply should I understand that pulling only one chain
without any restraints in only one direction will do my job? Please correct
me the mdp settings.


Do not pull along only one dimension. A normal, soluble protein complex 
will rotate in space so you should pull in all three dimensions. There 
are several ways to accomplish this pulling, but indeed you only need 
one reaction coordinate to induce separation.


-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!

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Re: [gmx-users] Pulling two groups in opposite direction

2018-05-17 Thread Naba 
On Thu, May 17, 2018 at 11:09 AM, Naba  wrote:

> On 5/16/18 3:32 AM, Naba wrote:
>> > Dear all,
>> >
>> > I am using gromacs 5.1.2 and trying to pull both monomers of 128 amino
>> > acids from its homodimer in opposite directions along z axis. The
>> > interfaces of each protein chain is parallel to the z axis. I do not
>> need
>> > any restraints in this case. I have gone through the GROMACS manual and
>> > some of the previous archived messages and set the following mdp
>> options.
>> >
>> > ; Pull code
>> > pull= yes
>> > pull_ngroups= 2
>> > pull_ncoords= 2
>> > pull_group1_name= chain_A
>> > pull_group2_name= chain_B
>> > ;pull_group3_name = Protein
>> > pull_coord1_type = umbrella
>> > pull_coord2_type = umbrella
>> > pull_coord1_init = 0.0
>> > pull_coord2_init = 0.0
>> > pull_coord1_start = yes   ; define initial COM distance > 0
>> > pull_coord2_start = yes
>> > pull_coord1_geometry= direction
>> > pull_coord2_geometry= direction
>> > pull_coord1_groups  = 2 1
>> > pull_coord2_groups  = 1 2
>> > pull_coord1_dim = N N Y
>> > pull_coord2_dim = N N Y
>>
>> Note that pull_coord*_dim is not relevant when using "direction" geometry.
>>
>> > pull_coord1_rate= 0.01; 0.008 nm per ps = 8 nm per ns
>> > pull_coord2_rate= 0.01 ; 0.008 nm per ps = 8 nm per ns
>> > pull_coord1_k   = 2000  ; kJ mol^-1 nm^-2
>> > pull_coord2_k   = 2000
>> > pull_coord1_vec= 0.0 0.0 1.0
>> > pull_coord2_vec= 0.0 0.0 -1.0
>> > nstcalcenergy = 1
>> > nhchainlength = 1
>> >
>> > But it fails to pull chain_A in positive z direction. However, chain_B
>> is
>> > seemed to pull in negative z direction. Someone please suggest the
>> proper
>> > way to pull two groups in opposite directions, or if there is anything
>> that
>> > I am missing.
>>
>> What is the point of pulling in two directions? Separation of two
>> species requires only one reaction coordinate. For every action, there
>> is an equal, but opposite reaction...
>>
>> -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
>>
>> ==
>
>
> Thank you Dr. Justin.
Besides PMF calculations during umbrella sampling, I want to observe the
interacting residues while pulling both the chain in opposite directions.
In your tutorial you pulled only one chain for your specific case. Whereas
in my case, the point to be observed how smoothly or rigorously the chains
are interacting with their residues in interface due to the application of
two equal forces in opposite directions.

Anyways, from your reply should I understand that pulling only one chain
without any restraints in only one direction will do my job? Please correct
me the mdp settings.


Nabajyoti Goswami

Research Associate
Bioinformatics Infrastructure Facility
Department of Animal Biotechnology
College of Veterinary Science
Khanapara,Guwahati 781022
Assam, India
-- 
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
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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Pulling two groups in opposite direction

2018-05-16 Thread Naba 
>
> On 5/16/18 3:32 AM, Naba wrote:
> > Dear all,
> >
> > I am using gromacs 5.1.2 and trying to pull both monomers of 128 amino
> > acids from its homodimer in opposite directions along z axis. The
> > interfaces of each protein chain is parallel to the z axis. I do not need
> > any restraints in this case. I have gone through the GROMACS manual and
> > some of the previous archived messages and set the following mdp options.
> >
> > ; Pull code
> > pull= yes
> > pull_ngroups= 2
> > pull_ncoords= 2
> > pull_group1_name= chain_A
> > pull_group2_name= chain_B
> > ;pull_group3_name = Protein
> > pull_coord1_type = umbrella
> > pull_coord2_type = umbrella
> > pull_coord1_init = 0.0
> > pull_coord2_init = 0.0
> > pull_coord1_start = yes   ; define initial COM distance > 0
> > pull_coord2_start = yes
> > pull_coord1_geometry= direction
> > pull_coord2_geometry= direction
> > pull_coord1_groups  = 2 1
> > pull_coord2_groups  = 1 2
> > pull_coord1_dim = N N Y
> > pull_coord2_dim = N N Y
>
> Note that pull_coord*_dim is not relevant when using "direction" geometry.
>
> > pull_coord1_rate= 0.01; 0.008 nm per ps = 8 nm per ns
> > pull_coord2_rate= 0.01 ; 0.008 nm per ps = 8 nm per ns
> > pull_coord1_k   = 2000  ; kJ mol^-1 nm^-2
> > pull_coord2_k   = 2000
> > pull_coord1_vec= 0.0 0.0 1.0
> > pull_coord2_vec= 0.0 0.0 -1.0
> > nstcalcenergy = 1
> > nhchainlength = 1
> >
> > But it fails to pull chain_A in positive z direction. However, chain_B is
> > seemed to pull in negative z direction. Someone please suggest the proper
> > way to pull two groups in opposite directions, or if there is anything
> that
> > I am missing.
>
> What is the point of pulling in two directions? Separation of two
> species requires only one reaction coordinate. For every action, there
> is an equal, but opposite reaction...
>
> -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
>
> ==



Thank you Dr. Justin.
Besides PMF calculations during umbrella sampling, I want to observe the
interacting residues while pulling both the chain in opposite directions.
In your tutorial you pulled only one chain for your specific case. Whereas
in my case, the point to be observed how smoothly or rigorously the chains
are interacting with their residues in interface due to the application of
two equal forces in opposite directions.

Anyways, from your reply should I understand that pulling only one chain
without any restraints in only one direction will do my job? Please correct
me the mdp settings.


Nabajyoti Goswami

Research Associate
Bioinformatics Infrastructure Facility
Department of Animal Biotechnology
College of Veterinary Science
Khanapara,Guwahati 781022
Assam, India
-- 
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
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mail to gmx-users-requ...@gromacs.org.

Re: [gmx-users] Pulling two groups in opposite direction

2018-05-16 Thread Justin Lemkul 



On 5/16/18 3:32 AM, Naba wrote:

Dear all,

I am using gromacs 5.1.2 and trying to pull both monomers of 128 amino
acids from its homodimer in opposite directions along z axis. The
interfaces of each protein chain is parallel to the z axis. I do not need
any restraints in this case. I have gone through the GROMACS manual and
some of the previous archived messages and set the following mdp options.

; Pull code
pull= yes
pull_ngroups= 2
pull_ncoords= 2
pull_group1_name= chain_A
pull_group2_name= chain_B
;pull_group3_name = Protein
pull_coord1_type = umbrella
pull_coord2_type = umbrella
pull_coord1_init = 0.0
pull_coord2_init = 0.0
pull_coord1_start = yes   ; define initial COM distance > 0
pull_coord2_start = yes
pull_coord1_geometry= direction
pull_coord2_geometry= direction
pull_coord1_groups  = 2 1
pull_coord2_groups  = 1 2
pull_coord1_dim = N N Y
pull_coord2_dim = N N Y


Note that pull_coord*_dim is not relevant when using "direction" geometry.


pull_coord1_rate= 0.01; 0.008 nm per ps = 8 nm per ns
pull_coord2_rate= 0.01 ; 0.008 nm per ps = 8 nm per ns
pull_coord1_k   = 2000  ; kJ mol^-1 nm^-2
pull_coord2_k   = 2000
pull_coord1_vec= 0.0 0.0 1.0
pull_coord2_vec= 0.0 0.0 -1.0
nstcalcenergy = 1
nhchainlength = 1

But it fails to pull chain_A in positive z direction. However, chain_B is
seemed to pull in negative z direction. Someone please suggest the proper
way to pull two groups in opposite directions, or if there is anything that
I am missing.


What is the point of pulling in two directions? Separation of two 
species requires only one reaction coordinate. For every action, there 
is an equal, but opposite reaction...


-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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[gmx-users] Pulling two groups in opposite direction

2018-05-16 Thread Naba 
Dear all,

I am using gromacs 5.1.2 and trying to pull both monomers of 128 amino
acids from its homodimer in opposite directions along z axis. The
interfaces of each protein chain is parallel to the z axis. I do not need
any restraints in this case. I have gone through the GROMACS manual and
some of the previous archived messages and set the following mdp options.

; Pull code
pull= yes
pull_ngroups= 2
pull_ncoords= 2
pull_group1_name= chain_A
pull_group2_name= chain_B
;pull_group3_name = Protein
pull_coord1_type = umbrella
pull_coord2_type = umbrella
pull_coord1_init = 0.0
pull_coord2_init = 0.0
pull_coord1_start = yes   ; define initial COM distance > 0
pull_coord2_start = yes
pull_coord1_geometry= direction
pull_coord2_geometry= direction
pull_coord1_groups  = 2 1
pull_coord2_groups  = 1 2
pull_coord1_dim = N N Y
pull_coord2_dim = N N Y
pull_coord1_rate= 0.01; 0.008 nm per ps = 8 nm per ns
pull_coord2_rate= 0.01 ; 0.008 nm per ps = 8 nm per ns
pull_coord1_k   = 2000  ; kJ mol^-1 nm^-2
pull_coord2_k   = 2000
pull_coord1_vec= 0.0 0.0 1.0
pull_coord2_vec= 0.0 0.0 -1.0
nstcalcenergy = 1
nhchainlength = 1

But it fails to pull chain_A in positive z direction. However, chain_B is
seemed to pull in negative z direction. Someone please suggest the proper
way to pull two groups in opposite directions, or if there is anything that
I am missing.

waiting for your great help..
Nabajyoti Goswami
Bioinformatics Infrastructure Facility
Department of Animal Biotechnology
College of Veterinary Science
Khanapara,Guwahati 781022
Assam, India
-- 
Gromacs Users mailing list

* Please search the archive at 
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* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

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