[gmx-users] DPPC to CG DPPC

[XAvier Periole]

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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