[gmx-users] md after digging a hole in the membrane

Itamar Kass ikass at cc.huji.ac.il
Sat Apr 19 16:27:00 CEST 2003

   Dear all, I try to use the DMPC bilayer from Tieleman's site in order to
produce a hole using Graham's modified mdrun.  The dimensions of the system (a
box of DMPC with water) are 6.176*6.176*6.6608 nm^3 (as given in the pdb file).
 In order to relaxed the system after digging a hole in it, I wanted to do some
MD (before entering my protein). 
   One of the variables I entered in the md.mdp file is "rcoulomb= 0.9", were
the coulomb interaction type was set to PME.  The grompp program replays "ERROR:
One of the box vectors is shorter than twice the cut-off length. Increase the
box size or decrease rcoulomb.".  Yes I know this is true, no need to tell me
this, my questions are: 
(i) Should I lower the rcoulomb parameter, and also the rlist and rvdw to ~6.1
nm?  Will the validity/reliability of the later simulation (which will be given
the same parameters) is going to change, using smaller rcoulomb,alist and rvdw
lower then 0.9nm (which is already low)? 
(ii) Should I enlarge the system by adding DMPC molecule and then solvated then?
 If yes, how can I do this easel?  I saw in the article of Faraldo-Gomez et. al.
(Eur. Biophys. J. 2002 Jun;31(3):217-27) that their systems were much bigger
then the one I use.  
(iii) Is there any place other then Tieleman's site where I can download DMPC
bilayer structures? 
       Thanks you all, Kass.

Computers are like airconditioners... They don't work well with Windows

| Itamar Kass
| The Alexander Silberman
| Institute of Life Sciences
| Department of Biological Chemistry
| The Hebrew University, Givat-Ram
| Jerusalem, 91904, Israel
| Tel: +972-(0)2-6585146
| Fax: +972-(0)2-6584329
| Email: ikass at cc.huji.ac.il
| Group Homepage: http://www.ls.huji.ac.il/~membranelab/

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