[gmx-users] mdrun Segmentation fault (after install make_hole_mdrun)

[Minghu Song]

Dear gmx users,

Recently I am using the modified make_hole version mdrun (thanks Dr. 
Smith) to make the
hole inthe lipid bilayer for membrane proteins.  The process of making 
hole itself
(mdrun -hole -holep *.mdp .....) worked  smoothly.  But today I found 
that I cannot run the
normal mdrun (except em process) anymore . For instance, the following is
the  results of simple MD simulation for 216 SPC water mentioned in 
tutorial:
 
mdrun  -s water.tpr -o water.trr  -c water_out.gro -v water.log
..................................................................................
Back Off! I just backed up md.log to ./#md.log.6#
Getting Loaded...
Reading file water.tpr, VERSION 3.1.4 (single precision)
Reading file water.tpr, VERSION 3.1.4 (single precision)
Loaded with Money
Back Off! I just backed up ener.edr to ./#ener.edr.13#
starting mdrun 'Pure Water'
5000 steps,     10.0 ps.
Back Off! I just backed up water.trr to ./#water.trr.7#
Back Off! I just backed up insidesurf.pdb to ./#insidesurf.pdb.11#
Segmentation fault
-------------------------

It seems that the line ".... insidesurf.pdb to ./#insidesurf.pdb.11#" 
should not apprear because I didn't the option -hole.
I re-configuration and compile them again, but the error still exists. 
 This is how I re-compiled today:
------------------------
make distclean
./configure
make
make install
make links
------------------------
 
Also, I have another question about the results from mdrun (make_hole 
version).  In the mdp file, I set up NPT ensemble (pcoupletype = 
anisotropic).
There is no any error reported after the calculation, but when I check 
the log file I found that the presssure is quite different as the setup 
one (1 bar):
mdrun -v -hole -holep hp.mdp  -deffnm insert
input run.mdp file:
----------------------------------------------------------------------
.....
Pcoupl                      =  berendsen
Pcoupltype               =  anisotropic
tau_p                        =  5
compressibility       =  4.5e-5  4.5e-5  4.5e-5  0   0   0
ref_p                        =  1.0       1.0       1.0       0   0   0
-----------------------------------------------------------------------

output in log file
-----------------------------------------------------------------------------------------------------------
Initial step 0:
Energies (kJ/mol)
          Angle    Proper Dih. Ryckaert-Bell.  Improper Dih.          LJ-14
    3.16511e+03    4.01188e+03    4.21941e+03    1.88532e+02    2.33083e+03
     Coulomb-14        LJ (SR)   Coulomb (SR)   Coulomb (LR) Position Rest.
    1.47721e+04   -4.50831e+03   -3.00000e+05   -2.99713e+03    2.42487e-02
      Potential    Kinetic En.        Total Energy       Temperature 
 Pressure (bar)
   -2.78818e+05    4.09423e+04   -2.37875e+05    2.99016e+02   
-3.39316e+03  (1bar ?)
                                                                        
                                     
last step 10000:
   Energies (kJ/mol)
          Angle    Proper Dih. Ryckaert-Bell.  Improper Dih.          LJ-14
    1.20003e+04    3.73106e+03    5.73505e+03    3.63259e+02    3.46746e+03
     Coulomb-14        LJ (SR)   Coulomb (SR)   Coulomb (LR) Position Rest.
    1.00511e+04    5.84592e+03   -2.99810e+05   -1.21922e+04    5.76862e+02
      Potential    Kinetic En.   Total Energy    Temperature       
Pressure (bar)
   -2.70231e+05    4.16222e+04   -2.28609e+05    3.03982e+02    4.94660e+02
--------------------------------------------------------------------------------------------------------
 
I just began to learn the MD as well as gromacs.  Maybe I made some 
"silly" mistakes duringing the installation step
or ask a very simple question.  Anyone help is greatly appreciated. 
Thanks inadvance.