From: Karol Kaszuba (
Date: Fri Oct 26 2007 - 04:57:35 CDT


 I am preparing 30ns simulation of big membrane x=130, y=130.
 In properly equilibrated membrane I will insert a model of GPCR.
 However I am not sure if a membrane of this size is still enough big for
 my receptor. The problem is that my model has a long cytoplasmatic loop
 and I am not sure about the mobility of this loop - does the loop will
 escape outside the membrane.
 The simulation of the bilayer will take a lot of time so I want to be sure
 that membrane will be big enough.

   I can solve this problem in two ways:
    - increase the membrane size - I do not want to do it,
    - move the receptor much more to the corner of bilayer.
 1) And here is my question - does the stability of a simulation will be
    influenced by the position of a protein. A picture with protein
    positioned in bilayer can be found at

2) Does the time of 30ns is sufficient to equilibrate a membrane of this
   size ?

3) In the work of Kandt et al, 2007 (full title below) I found that the
   protein cavities should be solvated however in the "Building Gramicidin
   tutorial" the HOH molecules that overlaped protein were removed - if I
   understand well overlap is not equal "to water which is inside but do not
   overlap with protein" - in conclusion - HOH molecules should fill the
   protein cavities - correct?
   Christian Kandt , Walter L Ash , D Peter Tieleman
   Methods. 2007 Apr ;41 (4):475-88 17367719
   Setting up and running molecular dynamics simulations of membrane proteins.

   Thank you in advance,


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