[gmx-users] Hydrogen molecule topology error

[Mark Abraham]

On 01/02/10 15:58, Nataraj wrote:
> 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

Manual section 7.4 lists the utility programs and groups them by topic. 
One of the "generating topologies and coordinates" programs does exactly 
this.

> 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 .

Neither can we. The things you posted are useless messages sent to 
stderr from the operating system. Read the tail of the .log file and the 
stdout.

> 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

That doesn't look right. vsite2 only allows function type 1 (see table 
in chapter 5)

Mark