[gmx-users] DPPC to CG DPPC

sunny mishra mishra.sunny at gmail.com
Tue Dec 15 18:21:21 CET 2009


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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