Re: [gmx-users] Simulation of ONLY Lipid Bilayer

[Anirban Ghosh]

On Thu, Apr 29, 2010 at 3:29 PM, Saumya  wrote:

> Hi all,
>
> I am using the pre-equilibriated layers from Tieleman. After the first
> energy minimization step, I removed the periodicity using trjconv. Now, in
> order to scale the lipid positions, I tried using Inflategro.
> Do I need to use strong position restraints (because that is for protein
> and I am just using the lipid bilayer)?
>

You want to scale the lipid positions to what? InflateGro is used to pack
the lipid molecules around a protein, but you want to simulate only lipids,
so no point in using it. If you want to simulate a lipid bilayer, you can
continue with one taken from Tieleman's site (but with what objective?).

>
> After the script is run, When I try doing the energy minimization, it shows
> unequal number of atoms in .gro and topology file. (the GRO Input has only
> lipid molecules where as topology files takes into account both SOL and
> lipid molecules).
>
How to remove this error?
>
>
InflateGro always removes all water (SOL) molecules. So you need to
resolvate the bilayer and update your .top file accordingly. Go through the
manual once.


> I am unable to find any tutorial that could guide through the steps and the
> parameters to be set while doing the simulation of only bilayers. Please
> suggest some tutorial.
>
> Kindly guide through the steps.
>
> Regards,
> Saumya
>
>
>
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Regards,

Anirban
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[gmx-users] Simulation of ONLY Lipid Bilayer

[Saumya]

Hi all,

I am using the pre-equilibriated layers from Tieleman. After the first
energy minimization step, I removed the periodicity using trjconv. Now, in
order to scale the lipid positions, I tried using Inflategro.
Do I need to use strong position restraints (because that is for protein and
I am just using the lipid bilayer)?

After the script is run, When I try doing the energy minimization, it shows
unequal number of atoms in .gro and topology file. (the GRO Input has only
lipid molecules where as topology files takes into account both SOL and
lipid molecules).
How to remove this error?

I am unable to find any tutorial that could guide through the steps and the
parameters to be set while doing the simulation of only bilayers. Please
suggest some tutorial.

Kindly guide through the steps.

Regards,
Saumya
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Re: [gmx-users] Simulation of only Lipid Bilayer

[Arun kumar V]

On Tue, Apr 6, 2010 at 5:05 PM, Justin A. Lemkul  wrote:

>
>
> Arun kumar V wrote:
>
>> Try PRODRG server to build the molecule as well as to get topology file.
>> Though  you might have to be careful in using this topology file.
>>
>>
> If by "be careful" you mean "don't use this topology," I'll agree :)  The
> Gromos parameters for lipids (at least Gromos87 and Gromos96 43a1, given by
> PRODRG) fall far short of reproducing lipid properties.  That, and the
> charges assigned by PRODRG for lipids will not resemble any known parameter
> set, requiring a complete re-write of this topology.  You could use PRODRG
> to build the molecule, but there are a number of other programs that can do
> that as well (see the Gromacs site for a list).
>
> To the original post: What lipid are you looking to simulate?  Many
> pre-equilibrated lipid bilayers are available in the public domain, along
> with suitable paramters, saving you a lot of work in building these systems.
>  They can be tricky.
>
> -Justin
>
>
> @Justin
 I agree with you. Currently I am not actively involving with
gromacs simulations but planning to involve. I have not been to GROMACS
website from long time. In fact the version I have used last time is gromacs
3.3(almost 2 years back). There is lot of progress ofcourse.

Thanks,
Arun

 Arun
>>
>> Saumya wrote:
>>
>>> Hi all,
>>>
>>> Well, I have been trying to make lipid bilayers using genconf of
>>> gromacs from a single lipid molecule.
>>> Can anyone tell me how to proceed with the simulation of lipid
>>> bilayers starting with a single lipid molecule?
>>> How can I obtain the .pdb file for a lipid?
>>> Is there any manual that describes the procedure using Gromacs?
>>>
>>> Hoping for some inputs.
>>>
>>> Regards
>>> Saumya
>>>
>>>
>>
>>
> --
> 
>
> 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
>
> 
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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>



-- 
Arun
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Re: [gmx-users] Simulation of only Lipid Bilayer

[Itamar Kass]

Hi Saumya,

for topology please look at those two paper from Poger in which he 
derive new parameters for various lipids:


1. Poger D., van Gunsteren W. F. & Mark A. E. (2009) A new force field 
for simulating phosphatidylcholine bilayers. J. Comput. Chem. in press 
(doi: 10.1002/jcc.21396)


2. Poger D. & Mark A. E. (2010) On the validation of molecular dynamics 
simulations of saturated and cis-monounsaturated phosphatidylcholine 
lipid bilayers: a comparison with experiment. J. Chem. Theory Comput. 6, 
325-336


A nice site to find coordinates for well equilibrated lipids is the one 
of Peter Tieleman 
 
(http://moose.bio.ucalgary.ca/).


Good luck with the simulations,
Itamar


On 6/04/10 9:35 PM, Justin A. Lemkul wrote:



Arun kumar V wrote:
Try PRODRG server to build the molecule as well as to get topology 
file. Though  you might have to be careful in using this topology file.




If by "be careful" you mean "don't use this topology," I'll agree :)  
The Gromos parameters for lipids (at least Gromos87 and Gromos96 43a1, 
given by PRODRG) fall far short of reproducing lipid properties.  
That, and the charges assigned by PRODRG for lipids will not resemble 
any known parameter set, requiring a complete re-write of this 
topology.  You could use PRODRG to build the molecule, but there are a 
number of other programs that can do that as well (see the Gromacs 
site for a list).


To the original post: What lipid are you looking to simulate?  Many 
pre-equilibrated lipid bilayers are available in the public domain, 
along with suitable paramters, saving you a lot of work in building 
these systems.  They can be tricky.


-Justin


Arun

Saumya wrote:

Hi all,

Well, I have been trying to make lipid bilayers using genconf of
gromacs from a single lipid molecule.
Can anyone tell me how to proceed with the simulation of lipid
bilayers starting with a single lipid molecule?
How can I obtain the .pdb file for a lipid?
Is there any manual that describes the procedure using Gromacs?

Hoping for some inputs.

Regards
Saumya






--


"In theory, there is no difference between theory and practice. But, in practice, 
there is." - Jan L.A. van de Snepscheut

===
| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
|
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Australia
|
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail: itamar.k...@med.monash.edu.au


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Re: [gmx-users] Simulation of only Lipid Bilayer

[Justin A. Lemkul]

Arun kumar V wrote:
Try PRODRG server to build the molecule as well as to get topology file. 
Though  you might have to be careful in using this topology file.




If by "be careful" you mean "don't use this topology," I'll agree :)  The Gromos 
parameters for lipids (at least Gromos87 and Gromos96 43a1, given by PRODRG) 
fall far short of reproducing lipid properties.  That, and the charges assigned 
by PRODRG for lipids will not resemble any known parameter set, requiring a 
complete re-write of this topology.  You could use PRODRG to build the molecule, 
but there are a number of other programs that can do that as well (see the 
Gromacs site for a list).


To the original post: What lipid are you looking to simulate?  Many 
pre-equilibrated lipid bilayers are available in the public domain, along with 
suitable paramters, saving you a lot of work in building these systems.  They 
can be tricky.


-Justin


Arun

Saumya wrote:

Hi all,

Well, I have been trying to make lipid bilayers using genconf of
gromacs from a single lipid molecule.
Can anyone tell me how to proceed with the simulation of lipid
bilayers starting with a single lipid molecule?
How can I obtain the .pdb file for a lipid?
Is there any manual that describes the procedure using Gromacs?

Hoping for some inputs.

Regards
Saumya
  




--


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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Re: [gmx-users] Simulation of only Lipid Bilayer

[Arun kumar V]

Try PRODRG server to build the molecule as well as to get topology file. 
Though  you might have to be careful in using this topology file.


Arun

Saumya wrote:

Hi all,

Well, I have been trying to make lipid bilayers using genconf of
gromacs from a single lipid molecule.
Can anyone tell me how to proceed with the simulation of lipid
bilayers starting with a single lipid molecule?
How can I obtain the .pdb file for a lipid?
Is there any manual that describes the procedure using Gromacs?

Hoping for some inputs.

Regards
Saumya
  


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[gmx-users] Simulation of only Lipid Bilayer

[Saumya]

Hi all,

Well, I have been trying to make lipid bilayers using genconf of
gromacs from a single lipid molecule.
Can anyone tell me how to proceed with the simulation of lipid
bilayers starting with a single lipid molecule?
How can I obtain the .pdb file for a lipid?
Is there any manual that describes the procedure using Gromacs?

Hoping for some inputs.

Regards
Saumya
-- 
gmx-users mailing listgmx-users@gromacs.org
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