[gmx-users] Simulation of only Lipid Bilayer

[Arun kumar V]

On Tue, Apr 6, 2010 at 5:05 PM, Justin A. Lemkul <jalemkul at vt.edu> 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
>
> ========================================
>
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-- 
Arun
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