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

Erik Lindahl lindahl at stanford.edu
Sat Apr 19 18:56:01 CEST 2003


I'm not quite sure which box you are talking about, since 6.18,6.18,6.66 
are all larger than 0.9 :-)

Perhaps it is a simple formatting error in the coordinate file?

In any case, a system with box dimensions in the size of 2nm might 
behave pretty strange with lipid molecules that themselves are 3 nm long.

By the way: rcoulomb isn't really a cutoff, since we do the rest in 
reciprocal space. You can always decrease rcoulomb and decrease the 
fourier grid spacing to do a more accurate sum in reciprocal space. 
(That would actually be an incredibly useful diploma work if somebody 
has an interested student - calculating a good set of accuracies for 
different cutoff and grid spacing combinations).



Itamar Kass wrote:

>   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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