[gmx-users] Hydrogen molecule topology error

[Nataraj]

Dear gmx-users,

I would like to perform a simulation of diffusion of
hydrogen molecule (H2) from surrounding water to the
protein interior. In this regard, I have the information of
partial charge of the hydrogen molecule from the literature
so I have developed my own 'itp' file with an assumption
 that the H2 molecule is connected with a dummy atom in a
linear fashion eg.,  H - D - H .

And as per the published protocol I have to add 100 such
molecules into the system, first of all I do not know how
to add randomly those molecules into my system (water +
protein) using any of the gromacs’ utility tool. So for an
trial, I have randomly gone by replacing a water molecule
(SOL at the end of my protein gro file)  with a hydrogen
molecule. 

And after those modification when I try to do energy
minimize the whole system, I receive the following error
and I tried without the newly added hydrogen and this time
the EM went on nice so it confirms that the error is lying
in the hydrogen addition but I could not figure out what it
cause for a memory error . 

I would be more glad if some one shed some light on this
issue. 
( Note:  I have also pasted the H2 molecule itp file
created by me hereunder after the error message )

With thanks,
B.Nataraj

*** glibc detected *** mdrun_d: realloc(): invalid next
size: 0x0a251800 ***
======= Backtrace: =========
/lib/tls/i686/cmov/libc.so.6[0xb7f713f4]
/lib/tls/i686/cmov/libc.so.6[0xb7f75051]
/lib/tls/i686/cmov/libc.so.6(realloc+0x106)[0xb7f75d86]
mdrun_d[0x81936ea]
======= Memory map: ========
08048000-08395000 r-xp 00000000 08:01 13527112
  /usr/local/gromacs/bin/mdrun_d
08395000-0839c000 rwxp 0034c000 08:01 13527112
  /usr/local/gromacs/bin/mdrun_d
0839c000-083a2000 rwxp 0839c000 00:00 0 
0a19b000-0a272000 rwxp 0a19b000 00:00 0          [heap]
b7200000-b7221000 rwxp b7200000 00:00 0 
b7221000-b7300000 ---p b7221000 00:00 0 
b7366000-b7382000 r-xp 00000000 08:01 1787343
   /lib/libgcc_s.so.1
b7382000-b7383000 rwxp 0001c000 08:01 1787343
   /lib/libgcc_s.so.1
b7390000-b7f02000 rwxp b7390000 00:00 0 
b7f02000-b805a000 r-xp 00000000 08:01 1803413
   /lib/tls/i686/cmov/libc-2.8.90.so
b805a000-b805c000 r-xp 00158000 08:01 1803413
   /lib/tls/i686/cmov/libc-2.8.90.so
b805c000-b805d000 rwxp 0015a000 08:01 1803413
   /lib/tls/i686/cmov/libc-2.8.90.so
b805d000-b8061000 rwxp b805d000 00:00 0 
b8061000-b8085000 r-xp 00000000 08:01 1803421
   /lib/tls/i686/cmov/libm-2.8.90.so
b8085000-b8086000 r-xp 00023000 08:01 1803421
   /lib/tls/i686/cmov/libm-2.8.90.so
b8086000-b8087000 rwxp 00024000 08:01 1803421
   /lib/tls/i686/cmov/libm-2.8.90.so
b8087000-b809c000 r-xp 00000000 08:01 1803424
   /lib/tls/i686/cmov/libnsl-2.8.90.so
b809c000-b809d000 r-xp 00014000 08:01 1803424
   /lib/tls/i686/cmov/libnsl-2.8.90.so
b809d000-b809e000 rwxp 00015000 08:01 1803424
   /lib/tls/i686/cmov/libnsl-2.8.90.so
b809e000-b80a0000 rwxp b809e000 00:00 0 
b80ac000-b80af000 rwxp b80ac000 00:00 0 
b80af000-b80c9000 r-xp 00000000 08:01 1785875
   /lib/ld-2.8.90.so
b80c9000-b80ca000 r-xp b80c9000 00:00 0          [vdso]
b80ca000-b80cb000 r-xp 0001a000 08:01 1785875
   /lib/ld-2.8.90.so
b80cb000-b80cc000 rwxp 0001b000 08:01 1785875
   /lib/ld-2.8.90.so
bfab6000-bfacb000 rwxp bffeb000 00:00 0          [stack]
Aborted

############## End of error #############

######### topology of hydrogen #########



; topology for hydrogen. 

[ moleculetype ]
;name    nrexcl
  H2       3

[ atoms ]
;   nr    type   resnr  residu    atom    cgnr
       charge     mass    ; total charge
     1     H       1     H2        H1      1
          0.475    1.00800  ; 0.00
     2     H       1     H2        H2      1
          0.475    1.00800  ; 0.00
     3     DUM     1     H2        DUM     1
         -0.950    0.00000
   
[ virtual_sites2 ]
; Site from funct a
3 1 2 2 0.7439756


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