[gmx-users] Pressure coupling for bilayer

[Anton Feenstra]

Itamar Kass wrote:

> 
> 
> itai bloch wrote:
> 
>> Hi all,
>>
>> I am trying to set up a simulation of peptide in lipid bilayer with a
>> file taken from Prof. Tieleman's website (dppc128.pdb). I used genbox
>> for the peptide positioning (which made quite a large cavity around
>> the peptide).

Yes - there is no other choice but to cut away all lipids that clash 
with your peptide - hence the cavities.

Alternatively, there is the mdrun_hole option which people have used 
with varying success. Search the list for 'hole' - I'd *not* advise 
using google ;-)

>> I have a problem of lipids molecules that go out of the bilayer while
>> doing the first position restrained run (only the peptide is fixed)
>> and from what I found in the mailing list it has to do with the
>> pressure coupling I use.
> 
>   Try to do some Md when the DMPC's phosphate atoms are fixed to the XY 
> plane.
> 
>> I have tried both isotropic and anisotropic coupling but it seems like
>> giving the same problem or just give an error due to large pressure
>> oscilations and halt the run.
>> Does anyone have suggestions from his own experience? I really need
>> help with it.

Try also first equilibrating without pressure coupling. In addition, you 
could 'squeeze' your conformation to approximately the right density 
first, using 'editconf -scale', and then equilibrate without pressure 
coupling. If this seem too harsh for you, you could also only scale the 
bilayer, and add back in the original, unscaled peptide at the proper 
location in the hole. Scaling will also make the holes between peptide 
and lipids a bit smaller.


-- 
Groetjes,

Anton

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|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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