[gmx-users] (no subject)

[Itamar Kass]

   Hi all, I try (hard) to make a hole in a lipid bilayer using the modified
mdrun by Graham R. Smith (thanks).  The compilation passed O.K. (when I entered
mdrun -h  I got info regarding the -hole option) upon Mandrake 9.0.
   The problem is thet whenever I try the debugsurf = yes option (in hpcyl.mdp)
I get no responce.  I try it becouse I have suspected thet mdrun does not even
read the hp*.mdp program I entered.  Can someone knows about it and can help me
to solve it?
   Moreover, as a results from the program I got a DMPC bilayer (taken basicly
from Tieleman) in which I have a hole.  The problem is thet I have some side
chaines of the DMPC in the hole, which I can not move out, no matter how much
minimization I do.


   Thanks you all, Itamar.


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Computers are like airconditioners... They don't work well with Windows open.
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| 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 vms.huji.ac.il
| Group Homepage: http://www.ls.huji.ac.il/~membranelab/
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