[gmx-users] About membrane protein

[Thomas Piggot]

Hi,

Are you sure that this is not just a visualisation artefact of the 
periodic boundary?

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions

Cheers

Tom

Justin Lemkul wrote:
> 
> 
> On 1/14/14, 2:13 PM, paulxie wrote:
>> Justin Lemkul wrote
>>>
>>> You will have to position the protein differently if it is oriented
>>> asymmetrically with respect the the membrane.  The same principles 
>>> apply,
>>> but
>>> box vectors will certainly be different, as will the editconf command.
>>>
>>> -Justin
>>>
>>> -
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or 
>>> send
>>> a mail to
>>
>>> gmx-users-request@
>>
>>> .
>>
>> Thanks Justin! It Is asymmetric because the protein consists of a
>> outer-membrane domain and a transmembrane helix. I placed the protein
>> asymmetrically to let the transmembrane helix in the middle of the 
>> bilayer
>> (dppc128) and adjusted the size of box. I confirmed that by checking the
>> coordinates in the system.gro and system_inflated.gro. But after that 
>> step,
>> after I did
>> " grompp -f minim.mdp -c system_inflated.gro -o confout.tpr -maxwarn 1"
>> and
>> "mdrun -deffnm confout -nt 1"
>> the coordinates of protein were dramatically changed, i.e. the protein 
>> was
>> totally away from the bilayer.
>> I think that should be something wrong, but cannot find it.
>>
> 
> Without seeing your exact commands, neither can anyone else.
> 
> -Justin
> 

-- 
Dr Thomas Piggot
University of Southampton, UK.