[gmx-users] mdrun_hole problems

Arvid Soderhall arvid at fmp-berlin.de
Thu Jan 29 16:08:00 CET 2004

Hi all 
I am about to start use the G. Smith and J Faraldo-Gomez membrane hole
maker but it does not run properly. 
At first I am able to do a few steepest descent steps with the
mdrun_hole, but when I switch to "integrator = md" the program stops
when its just about to do the first step. The error message is simply
"segmentation fault". 

To test if the problem is within the system I tried to do the same thing
with the normal mdrun (gromacs 3.1.4) and then it runs smooth.  

I have used the same compilation flags for both mdrun and mdrun_hole: 
export CFLAGS="-O6 -fomit-frame-pointer -finline-functions -Wall
-Wno-unused -malign-double -funroll-all-loops"

Here is also a copy of the hp.mdp file (which is almost a copy of the
one in the tutorial)
holetype                 = MSMS
hfm                      = 10
supf                     = 10
molsurf_log              = gsurf.log 
hr			 = 0 
hx			 = 0
hy			 = 0 
hz			 = 0.0
hp1 			 = 1
hp2 			 = 5600
s1 			 = 5601
s2			 = 16565
hz1 			 = -1.7
hz2 			 = 1.7
sfm 			 = 5.0 
sofs			 = 0.15 
molsurf_file             =
debugsurf 		 = no
resforces  		 = yes

Any suggestions what might be wrong? Compilation/installation/setup?

Thanx in advance


Arvid Soederhaell, PhD                              
Forschungsinstitut fuer Molekulare Pharmakologie    
Robert-Roessle-Strasse 10                           
131 25 Berlin

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