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

[Xavier Periole]

Hi,

You better check the actual definition of your system.
Generate a conf.gro from your conf.pdb abd check the
size (last line of the file). 0.9 nm is certainly not more than
half of 6.1 nm.
If you define your size box as 6.176*6.176*6.6608 in the
pdb it is interpreted in Angstroms ...

Xavier


On Saturday, April 19, 2003, at 10:26  am, 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
> open.
> ********************************************
>
> ===========================================
> | 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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