[gmx-users] DPPC to CG DPPC

[XAvier Periole]

For the steps to go through to have an embedded protein in
membrane bilayer Justin has made a nice tutorial ... look in
the mail list archive

On Dec 15, 2009, at 6:21 PM, sunny mishra wrote:

> ok. Thats the step where I am really confused that how to apply the  
> PR on my system file (system file is a combination of CG protein and  
> CG lipid).
>
> On Tue, Dec 15, 2009 at 12:16 PM, XAvier Periole <x.periole at rug.nl>  
> wrote:
>
> Well if you put a protein CG into your DPPC bilayer you'll have to
> be soft on the start. PR is one way to do it and you can do similar
> to when doing on a atomistic simulation.
>
> On Dec 15, 2009, at 6:13 PM, sunny mishra wrote:
>
>> Alright thanks. So should I do it for proteins?
>>
>> On Tue, Dec 15, 2009 at 12:12 PM, XAvier Periole <x.periole at rug.nl>  
>> wrote:
>>
>> No need of position restrained simulation with the CG lipids.
>> CG is very forgiving :))
>>
>> For proteins it is more delicate.
>>
>> On Dec 15, 2009, at 6:02 PM, sunny mishra wrote:
>>
>>> Thanks for the reply. I have another quick question that If I have  
>>> to do the Position Restrained EM Simulation of CG DPPC lipid then  
>>> is it done the same way we do for atomistic structure of proteins  
>>> like by defining the LIPPOSRES in the lipid.mdp file or while  
>>> using MARTINI forcefield is there any other way of doing the  
>>> Position Restrained EM simulation of CG DPPC lipids?
>>>
>>> On Tue, Dec 15, 2009 at 10:55 AM, XAvier Periole  
>>> <x.periole at rug.nl> wrote:
>>> I have downloaded the 128 DPPC lipid molecules from Dr. Tielmen's  
>>> Website and I am trying to convert the Atomistic structure to CG  
>>> structure. For that I am using atom2cg script provided by the  
>>> martini folks but it doesn't convert the Atomistic structure to CG  
>>> structure. atom2cg script works well for converting the atomistic  
>>> structure of PROTEIN to CG structure of protein but for LIPIDS it  
>>> doesn't work. Does anyone know how can I convert the 128 DPPC  
>>> atomistic structure of lipids to CG structure.
>>>
>>> This is correct. atom2cg is only working for proteins ...
>>>
>>> I would suggest you take dppc structure file from the martini web  
>>> site!
>>>
>>> Best Regards,
>>>
>>> Sunny
>>>
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