Re: [gmx-users] Fluctuation from mean position in one direction

[Mark Abraham]

On 19/07/2011 12:16 PM, Sławomir Stachura wrote:

Hi GMX-Users,
I am analysing my POPC membrane simulation and I want to calculate average 
fluctuation from mean postion of POPC lipids in perpendicular direction to 
membrane surface (Z-direction) to grasp that kind of motion. I've searched 
through mailing list and manual, but couldn't find any solution. Maybe someone 
has an idea how to achieve that? I'd be grateful for any help.


Since there exists no shrink-wrapped solution, you'll have to develop 
one. Express mathematically what you want to observe, and then consider 
how g_traj and g_analyze might be used to achieve it.


Mark
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[gmx-users] Fluctuation from mean position in one direction

[Sławomir Stachura]

Hi GMX-Users,
I am analysing my POPC membrane simulation and I want to calculate average 
fluctuation from mean postion of POPC lipids in perpendicular direction to 
membrane surface (Z-direction) to grasp that kind of motion. I've searched 
through mailing list and manual, but couldn't find any solution. Maybe someone 
has an idea how to achieve that? I'd be grateful for any help.
Best wishes,
Slawomir Stachura   



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[gmx-users] Voronoi tessellation

[francesca . stanzione]

  Hi all,

  Is my first time with phospholipids and I have questions about the  
Voronoi tessellation. I made a simulation of membrane with the  
insertion of fatty acids. Now I wanna calculate the 2D-Voronoi, but I  
don't know how can I make it. Do I need to choice some atoms? What  
kind of atoms? I need to check the xy coordinates of these atoms from  
the average structure or for each picosecond? If someone can explain  
me this analysis I'll  appreciate, in alternative, could you suggest  
me a good article able to help me with this analyses? Thanx, Francesca
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Re: [gmx-users] simulation of oligomers/monomers

[Justin A. Lemkul]

Kavyashree M wrote:

Sir,

My aim was to find out the difference between the monomer protein and
monomer of the dimer. it was for a preliminary analysis of the dynamics of
the structure and not a detailed study. But whatever the aim is, if the 
protein is

stable during the simulation then can a comparison be made for the dynamics
of protein from different sources.



If stability is not an issue, then maybe you can do some assessment.  Perhaps 
dimerization (or higher oligomerization) is needed to impart coordinated motion 
for catalysis; there are many such examples.  This will require a fairly 
detailed approach like PCA to uncover, rather than some cursory examination of 
dynamics.  What you need is a well-defined question that you can answer with the 
tools available to you.


-Justin


Thank you
With Regards
M. Kavyashree

On Mon, Jul 18, 2011 at 6:22 PM, Ragothaman Yennamalli 
mailto:ragotha...@gmail.com>> wrote:


With regards to run a monomeric simulation as resonable or not, I
would agree with Mark that it depends what you wish to learn, and
depends on what your hypothesis is.
Ragothaman

On Mon, Jul 18, 2011 at 7:49 AM, Kavyashree M mailto:hmkv...@gmail.com>> wrote:

Thank you Sir,

The interface is connected by salt bridges and hydrogen bonding
interactions and not severely
hydrophobic. I tried simulating the monomers it stayed quite
stable without unfolding till 50ns.
Even the other structure which are reported to be dimer is a
reported as a trimer in solution.
Another one is a part of a bifunctional protein which is an
octamer. So Because of all these
confusions I through some information could be obtained from a
monomeric simulation..
Is it reasonable?


Thanking you
With Regards
M. Kavyashree

On Mon, Jul 18, 2011 at 6:02 PM, Ragothaman Yennamalli
mailto:ragotha...@gmail.com>> wrote:

Look at this paper where the simulation was done on a
protein dimer:
http://www.ncbi.nlm.nih.gov/pubmed/17027497

On Mon, Jul 18, 2011 at 2:50 AM, Mark Abraham
mailto:mark.abra...@anu.edu.au>>
wrote:

On 18/07/2011 3:08 PM, Kavyashree M wrote:

Dear users,

I am working on a protein which is a dimer (in the
crystal structure), predicted according top PISA.
and some of the homologous proteins are dimers
(covalent /non-covalent) some are monomers.
There has not been any literature regarding the fact
that the functional unit is a dimer, ie the enzyme
is not functional when the dimeric interface is
disturbed due to mutations. Also the active sites
are not
shared among the dimeric partners. In this situation
is it meningful to do a simulation of monomers alone
and try to get some information.


The dimeric interface might be so hydrophobic the
protein would unfold - but unlikely given the homology
evidence. It could certainly perturb the structure
significantly, and perhaps such perturbations connect
with the activity. Only detailed understanding of the
structure and function can help you decide about this.


In general is it necessary to simulate only the
functional oligomers or monomer also can be done ?


Depends on the system, and depends what you wish to learn.

Mark
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Re: [gmx-users] simulation of oligomers/monomers

[Kavyashree M]

Sir,

My aim was to find out the difference between the monomer protein and
monomer of the dimer. it was for a preliminary analysis of the dynamics of
the structure and not a detailed study. But whatever the aim is, if the
protein is
stable during the simulation then can a comparison be made for the dynamics
of protein from different sources.

Thank you
With Regards
M. Kavyashree

On Mon, Jul 18, 2011 at 6:22 PM, Ragothaman Yennamalli  wrote:

> With regards to run a monomeric simulation as resonable or not, I would
> agree with Mark that it depends what you wish to learn, and depends on what
> your hypothesis is.
> Ragothaman
>
> On Mon, Jul 18, 2011 at 7:49 AM, Kavyashree M  wrote:
>
>> Thank you Sir,
>>
>> The interface is connected by salt bridges and hydrogen bonding
>> interactions and not severely
>> hydrophobic. I tried simulating the monomers it stayed quite stable
>> without unfolding till 50ns.
>> Even the other structure which are reported to be dimer is a reported as a
>> trimer in solution.
>> Another one is a part of a bifunctional protein which is an octamer. So
>> Because of all these
>> confusions I through some information could be obtained from a monomeric
>> simulation..
>> Is it reasonable?
>>
>>
>> Thanking you
>> With Regards
>> M. Kavyashree
>>
>> On Mon, Jul 18, 2011 at 6:02 PM, Ragothaman Yennamalli <
>> ragotha...@gmail.com> wrote:
>>
>>> Look at this paper where the simulation was done on a protein dimer:
>>> http://www.ncbi.nlm.nih.gov/pubmed/17027497
>>>
>>> On Mon, Jul 18, 2011 at 2:50 AM, Mark Abraham 
>>> wrote:
>>>
 On 18/07/2011 3:08 PM, Kavyashree M wrote:

> Dear users,
>
> I am working on a protein which is a dimer (in the crystal structure),
> predicted according top PISA.
> and some of the homologous proteins are dimers (covalent /non-covalent)
> some are monomers.
> There has not been any literature regarding the fact that the
> functional unit is a dimer, ie the enzyme
> is not functional when the dimeric interface is disturbed due to
> mutations. Also the active sites are not
> shared among the dimeric partners. In this situation is it meningful to
> do a simulation of monomers alone
> and try to get some information.
>

 The dimeric interface might be so hydrophobic the protein would unfold -
 but unlikely given the homology evidence. It could certainly perturb the
 structure significantly, and perhaps such perturbations connect with the
 activity. Only detailed understanding of the structure and function can 
 help
 you decide about this.


  In general is it necessary to simulate only the functional oligomers or
> monomer also can be done ?
>

 Depends on the system, and depends what you wish to learn.

 Mark
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Re: [gmx-users] GPUs and umbrella sampling

[XAvier Periole]

Yes, include the harmonic restrain(s) directly into the topology. Then  
you may
convert the info (distance(s), angle(s)) into the g_wham format  
(which  I do not
know but should be reasonably easy) or use another script to get your  
PMF or

make you own ... it is possible.

On Jul 18, 2011, at 9:37 AM, Guido Polles wrote:


Hi everybody,
 I noticed that GPU version of gromacs do not support the pull code,
hence i suppose g_wham cannot be used to extract a PMF. I would like
to just ask if somebody could suggest or give any hint about the way
to do umbrella sampling and extract a PMF without pull code, so that I
will have an idea before I start diving deeper into the issue, make
mistakes and potentially write useless code.
Thanks in advance for any advice.
Guido Polles
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[gmx-users] GPUs and umbrella sampling

[Guido Polles]

Hi everybody,
  I noticed that GPU version of gromacs do not support the pull code,
hence i suppose g_wham cannot be used to extract a PMF. I would like
to just ask if somebody could suggest or give any hint about the way
to do umbrella sampling and extract a PMF without pull code, so that I
will have an idea before I start diving deeper into the issue, make
mistakes and potentially write useless code.
Thanks in advance for any advice.
Guido Polles
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Re: [gmx-users] applying harmonic restraint

[Justin A. Lemkul]

devawati dutta wrote:

Dear sir
I want to apply harmonic restraint to the entire structure by 2.4 
kcal/mol/A and will perform energy minimization by steepest descent 
method followed by 100 ps simulation for DNA-drug complex.I need to 
reduce the harmonic restaint slowly to zero by decreasing the force 
constant value. But I don't know where to decrease the force constant 
value. Where i will reduce the value in .mdp file? How can I apply 
harmonic restraint in whole structure?




There is no automated way to decrease the force constant of a restraint.  The 
best option is to decrease it manually by using .mdp files that specify a short 
number of steps and conditionals in the topology (i.e. #ifdef statements 
triggered by the "define" keyword in the .mdp file).


-Justin

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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[gmx-users] applying harmonic restraint

[devawati dutta]

Dear sir
I want to apply harmonic restraint to the entire structure by 2.4 kcal/mol/A
and will perform energy minimization by steepest descent method followed by
100 ps simulation for DNA-drug complex.I need to reduce the harmonic
restaint slowly to zero by decreasing the force constant value. But I don't
know where to decrease the force constant value. Where i will reduce the
value in .mdp file? How can I apply harmonic restraint in whole structure?

-- 
With regards,
Devawati Dutta,
MSc,MTech(Bioinformatics),
Project Assistant Level-III
Infectious Diseases and Immunology Division
Indian Institute of Chemical Biology (A Unit of CSIR)
Kolkata-32.
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Re: [gmx-users] simulation of oligomers/monomers

[Ragothaman Yennamalli]

With regards to run a monomeric simulation as resonable or not, I would
agree with Mark that it depends what you wish to learn, and depends on what
your hypothesis is.
Ragothaman

On Mon, Jul 18, 2011 at 7:49 AM, Kavyashree M  wrote:

> Thank you Sir,
>
> The interface is connected by salt bridges and hydrogen bonding
> interactions and not severely
> hydrophobic. I tried simulating the monomers it stayed quite stable without
> unfolding till 50ns.
> Even the other structure which are reported to be dimer is a reported as a
> trimer in solution.
> Another one is a part of a bifunctional protein which is an octamer. So
> Because of all these
> confusions I through some information could be obtained from a monomeric
> simulation..
> Is it reasonable?
>
>
> Thanking you
> With Regards
> M. Kavyashree
>
> On Mon, Jul 18, 2011 at 6:02 PM, Ragothaman Yennamalli <
> ragotha...@gmail.com> wrote:
>
>> Look at this paper where the simulation was done on a protein dimer:
>> http://www.ncbi.nlm.nih.gov/pubmed/17027497
>>
>> On Mon, Jul 18, 2011 at 2:50 AM, Mark Abraham wrote:
>>
>>> On 18/07/2011 3:08 PM, Kavyashree M wrote:
>>>
 Dear users,

 I am working on a protein which is a dimer (in the crystal structure),
 predicted according top PISA.
 and some of the homologous proteins are dimers (covalent /non-covalent)
 some are monomers.
 There has not been any literature regarding the fact that the functional
 unit is a dimer, ie the enzyme
 is not functional when the dimeric interface is disturbed due to
 mutations. Also the active sites are not
 shared among the dimeric partners. In this situation is it meningful to
 do a simulation of monomers alone
 and try to get some information.

>>>
>>> The dimeric interface might be so hydrophobic the protein would unfold -
>>> but unlikely given the homology evidence. It could certainly perturb the
>>> structure significantly, and perhaps such perturbations connect with the
>>> activity. Only detailed understanding of the structure and function can help
>>> you decide about this.
>>>
>>>
>>>  In general is it necessary to simulate only the functional oligomers or
 monomer also can be done ?

>>>
>>> Depends on the system, and depends what you wish to learn.
>>>
>>> Mark
>>> --
>>> gmx-users mailing listgmx-users@gromacs.org
>>> http://lists.gromacs.org/**mailman/listinfo/gmx-users
>>> Please search the archive at http://www.gromacs.org/**
>>> Support/Mailing_Lists/Searchbefore
>>>  posting!
>>> Please don't post (un)subscribe requests to the list. Use the www
>>> interface or send it to gmx-users-requ...@gromacs.org.
>>> Can't post? Read 
>>> http://www.gromacs.org/**Support/Mailing_Lists
>>>
>>
>>
>>
>>
>> --
>>
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
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>
>
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Re: [gmx-users] simulation of oligomers/monomers

[Kavyashree M]

Thank you Sir,

The interface is connected by salt bridges and hydrogen bonding interactions
and not severely
hydrophobic. I tried simulating the monomers it stayed quite stable without
unfolding till 50ns.
Even the other structure which are reported to be dimer is a reported as a
trimer in solution.
Another one is a part of a bifunctional protein which is an octamer. So
Because of all these
confusions I through some information could be obtained from a monomeric
simulation..
Is it reasonable?

Thanking you
With Regards
M. Kavyashree

On Mon, Jul 18, 2011 at 6:02 PM, Ragothaman Yennamalli  wrote:

> Look at this paper where the simulation was done on a protein dimer:
> http://www.ncbi.nlm.nih.gov/pubmed/17027497
>
> On Mon, Jul 18, 2011 at 2:50 AM, Mark Abraham wrote:
>
>> On 18/07/2011 3:08 PM, Kavyashree M wrote:
>>
>>> Dear users,
>>>
>>> I am working on a protein which is a dimer (in the crystal structure),
>>> predicted according top PISA.
>>> and some of the homologous proteins are dimers (covalent /non-covalent)
>>> some are monomers.
>>> There has not been any literature regarding the fact that the functional
>>> unit is a dimer, ie the enzyme
>>> is not functional when the dimeric interface is disturbed due to
>>> mutations. Also the active sites are not
>>> shared among the dimeric partners. In this situation is it meningful to
>>> do a simulation of monomers alone
>>> and try to get some information.
>>>
>>
>> The dimeric interface might be so hydrophobic the protein would unfold -
>> but unlikely given the homology evidence. It could certainly perturb the
>> structure significantly, and perhaps such perturbations connect with the
>> activity. Only detailed understanding of the structure and function can help
>> you decide about this.
>>
>>
>>  In general is it necessary to simulate only the functional oligomers or
>>> monomer also can be done ?
>>>
>>
>> Depends on the system, and depends what you wish to learn.
>>
>> Mark
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/**mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/**
>> Support/Mailing_Lists/Searchbefore
>>  posting!
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>>
>
>
>
>
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Re: [gmx-users] simulation of oligomers/monomers

[Ragothaman Yennamalli]

Look at this paper where the simulation was done on a protein dimer:
http://www.ncbi.nlm.nih.gov/pubmed/17027497

On Mon, Jul 18, 2011 at 2:50 AM, Mark Abraham wrote:

> On 18/07/2011 3:08 PM, Kavyashree M wrote:
>
>> Dear users,
>>
>> I am working on a protein which is a dimer (in the crystal structure),
>> predicted according top PISA.
>> and some of the homologous proteins are dimers (covalent /non-covalent)
>> some are monomers.
>> There has not been any literature regarding the fact that the functional
>> unit is a dimer, ie the enzyme
>> is not functional when the dimeric interface is disturbed due to
>> mutations. Also the active sites are not
>> shared among the dimeric partners. In this situation is it meningful to do
>> a simulation of monomers alone
>> and try to get some information.
>>
>
> The dimeric interface might be so hydrophobic the protein would unfold -
> but unlikely given the homology evidence. It could certainly perturb the
> structure significantly, and perhaps such perturbations connect with the
> activity. Only detailed understanding of the structure and function can help
> you decide about this.
>
>
>  In general is it necessary to simulate only the functional oligomers or
>> monomer also can be done ?
>>
>
> Depends on the system, and depends what you wish to learn.
>
> Mark
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users
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> Support/Mailing_Lists/Searchbefore
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[gmx-users] Fwd: inquiry

[Rossen Apostolov]

Please send your mails directly to the mailing list 
gmx-users@gromacs.org (cc:).


Rossen

 Original Message 
Subject:inquiry
Date:   Sun, 17 Jul 2011 01:26:18 -0700
From:   sara soleimanzadegan 
Reply-To:   sara soleimanzadegan 
To: gmx-users-ow...@gromacs.org 



Dear Gromacs users,

I'm a beginner in Gromacs and I want to work with martini coarse-grained 
about surfactant.
I studied the tutorial of MARTINI website for protein in water and dspc 
lipid and etc but I'm a little bit confuse about the .gro file for 
surfactant. May I know how do produce .gro file for CG structure for 
surfactant (for example sds) and what are its steps?

please help me.

Regards

S. Soleimanzadegan
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Re: [gmx-users] simulation of oligomers/monomers

[Mark Abraham]

On 18/07/2011 3:08 PM, Kavyashree M wrote:

Dear users,

I am working on a protein which is a dimer (in the crystal structure), 
predicted according top PISA.
and some of the homologous proteins are dimers (covalent 
/non-covalent) some are monomers.
There has not been any literature regarding the fact that the 
functional unit is a dimer, ie the enzyme
is not functional when the dimeric interface is disturbed due to 
mutations. Also the active sites are not
shared among the dimeric partners. In this situation is it meningful 
to do a simulation of monomers alone

and try to get some information.


The dimeric interface might be so hydrophobic the protein would unfold - 
but unlikely given the homology evidence. It could certainly perturb the 
structure significantly, and perhaps such perturbations connect with the 
activity. Only detailed understanding of the structure and function can 
help you decide about this.


In general is it necessary to simulate only the functional oligomers 
or monomer also can be done ?


Depends on the system, and depends what you wish to learn.

Mark
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