[gmx-users] Re: Creating a monolayer from Martini bilayer

[Neha]

Hi Tsjerk,

Thank you so much for being so patient!
I have yet another question. The membrane I got from the Martini website
already has water in it. Do I need to add more water and if so why?

Also how exactly do I use trjconv to put all molecules in the box? Sorry for
being so annoying need a lot of elaboration!


Tsjerk Wassenaar wrote
> Hi Neha,
> 
> A single structure is like a trajectory with only one frame :p trjconv
> works on those as well.
> Right, set the center at 0,0,0 and choose the lipids as group for
> centering.
> 
> Cheers,
> 
> Tsjerk
> 
> 
> On Mon, Jun 3, 2013 at 7:31 PM, Neha <

> nshafique@

> > wrote:
> 
>> Hi, thank you so much!
>>
>> This way seems promising, however I am not sure how to center the bilayer
>> around z=0. I thought I could use editconf but I might be confused as to
>> how
>> Gromacs centers its objects. If I put -center 0 0 0 does that mean the
>> bilayer is centered around z = 0?
>>
>> Also I thought that trjconv only dealt with trajectory files. What I have
>> right now is a structure file, a topology file and an map file. After I
>> have
>> solvated, I will still only have a new structure file, so what would the
>> trjconv be acting on?
>>
>> Thank you so much for helping out a newbie!
>>
>>
>> Hey :)
>>
>> Just center the bilayer around z=0, solvate and put all molecules in the
>> box with trjconv. Then add 10 to the PBC Z-component (third number from
>> the
>> last line in the .gro file).
>>
>> Cheers,
>>
>> Tsjerk
>>
>>
>>
>>
>>
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> 
> 
> -- 
> Tsjerk A. Wassenaar, Ph.D.
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