[gmx-users] g_density fails after calculating for the last snapshot

[Christopher Neale]

What output do you get from gmxcheck -f martin_md_290K_100ns_tau1.xtc ? Also, can you extract that problematic frame with trjconv and run g_density on that one frame (what happens?). Also, can you make a new .xtc that is missing that last frame and see what g_density does?

These will help you to figure out what is going on.

Chris.

-- original message --
	
Hi All
I have a 100 ns lipid simulation for which I want the density profile. I issued the following command

g_density -f martin_md_290K_100ns_tau1.xtc -n dppc.ndx -s martin_md_290K_100ns_tau1.tpr -o water_density.xvg -b 50000

The program fails with the following message

Selected 3: 'Water'
Last frame      25000 time 100000.000  
*** glibc detected *** g_density: munmap_chunk(): invalid pointer: 0x0000000000d655d0 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x7eb96)[0x7fb120a73b96]
/usr/lib/libgmxana.so.6(calc_density+0x30c)[0x7fb120e14bec]
/usr/lib/libgmxana.so.6(gmx_density+0x42b)[0x7fb120e1541b]
g_density(main+0x9)[0x400629]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xed)[0x7fb120a1676d]
g_density[0x400659]
======= Memory map: ========
00400000-00401000 r-xp 00000000 08:06 4099695                            /usr/bin/g_density
00600000-00601000 r--p 00000000 08:06 4099695                            /usr/bin/g_density
00601000-00602000 rw-p 00001000 08:06 4099695                            /usr/bin/g_density
00d57000-00e57000 rw-p 00000000 00:00 0                                  [heap]
7fb11f003000-7fb11f018000 r-xp 00000000 08:06 3014802                    /lib/x86_64-linux-gnu/libgcc_s.so.1
7fb11f018000-7fb11f217000 ---p 00015000 08:06 3014802                    /lib/x86_64-linux-gnu/libgcc_s.so.1
7fb11f217000-7fb11f218000 r--p 00014000 08:06 3014802                    /lib/x86_64-linux-gnu/libgcc_s.so.1
7fb11f218000-7fb11f219000 rw-p 00015000 08:06 3014802                    /lib/x86_64-linux-gnu/libgcc_s.so.1
7fb11f239000-7fb11f26c000 rw-p 00000000 00:00 0
7fb11f26c000-7fb11f282000 r-xp 00000000 08:06 3015169                    /lib/x86_64-linux-gnu/libz.so.1.2.3.4
7fb11f282000-7fb11f481000 ---p 00016000 08:06 3015169                    /lib/x86_64-linux-gnu/libz.so.1.2.3.4
7fb11f481000-7fb11f482000 r--p 00015000 08:06 3015169                    /lib/x86_64-linux-gnu/libz.so.1.2.3.4
7fb11f482000-7fb11f483000 rw-p 00016000 08:06 3015169                    /lib/x86_64-linux-gnu/libz.so.1.2.3.4
7fb11f483000-7fb11f485000 r-xp 00000000 08:06 3014907                    /lib/x86_64-linux-gnu/libdl-2.15.so
7fb11f485000-7fb11f685000 ---p 00002000 08:06 3014907                    /lib/x86_64-linux-gnu/libdl-2.15.so
7fb11f685000-7fb11f686000 r--p 00002000 08:06 3014907                    /lib/x86_64-linux-gnu/libdl-2.15.so
7fb11f686000-7fb11f687000 rw-p 00003000 08:06 3014907                    /lib/x86_64-linux-gnu/libdl-2.15.so
7fb11f687000-7fb11f7d8000 r-xp 00000000 08:06 4070629                    /usr/lib/x86_64-linux-gnu/libxml2.so.2.7.8
7fb11f7d8000-7fb11f9d7000 ---p 00151000 08:06 4070629                    /usr/lib/x86_64-linux-gnu/libxml2.so.2.7.8
7fb11f9d7000-7fb11f9df000 r--p 00150000 08:06 4070629                    /usr/lib/x86_64-linux-gnu/libxml2.so.2.7.8
7fb11f9df000-7fb11f9e1000 rw-p 00158000 08:06 4070629                    /usr/lib/x86_64-linux-gnu/libxml2.so.2.7.8
7fb11f9e1000-7fb11f9e2000 rw-p 00000000 00:00 0
7fb11f9e2000-7fb11fb46000 r-xp 00000000 08:06 4064740                    /usr/lib/libfftw3f.so.3.3.0
7fb11fb46000-7fb11fd45000 ---p 00164000 08:06 4064740                    /usr/lib/libfftw3f.so.3.3.0
7fb11fd45000-7fb11fd51000 r--p 00163000 08:06 4064740                    /usr/lib/libfftw3f.so.3.3.0
7fb11fd51000-7fb11fd52000 rw-p 0016f000 08:06 4064740                    /usr/lib/libfftw3f.so.3.3.0
7fb11fd52000-7fb11fe4d000 r-xp 00000000 08:06 3014916                    /lib/x86_64-linux-gnu/libm-2.15.so
7fb11fe4d000-7fb12004c000 ---p 000fb000 08:06 3014916                    /lib/x86_64-linux-gnu/libm-2.15.so
7fb12004c000-7fb12004d000 r--p 000fa000 08:06 3014916                    /lib/x86_64-linux-gnu/libm-2.15.so
7fb12004d000-7fb12004e000 rw-p 000fb000 08:06 3014916                    /lib/x86_64-linux-gnu/libm-2.15.so
7fb12004e000-7fb120066000 r-xp 00000000 08:06 3014910                    /lib/x86_64-linux-gnu/libpthread-2.15.so
7fb120066000-7fb120265000 ---p 00018000 08:06 3014910                    /lib/x86_64-linux-gnu/libpthread-2.15.so
7fb120265000-7fb120266000 r--p 00017000 08:06 3014910                    /lib/x86_64-linux-gnu/libpthread-2.15.so
7fb120266000-7fb120267000 rw-p 00018000 08:06 3014910                    /lib/x86_64-linux-gnu/libpthread-2.15.so
7fb120267000-7fb12026b000 rw-p 00000000 00:00 0
7fb12026b000-7fb1204f9000 r-xp 00000000 08:06 4099651                    /usr/lib/libgmx.so.6
7fb1204f9000-7fb1206f8000 ---p 0028e000 08:06 4099651                    /usr/lib/libgmx.so.6
7fb1206f8000-7fb1206fe000 r--p 0028d000 08:06 4099651                    /usr/lib/libgmx.so.6
7fb1206fe000-7fb120707000 rw-p 00293000 08:06 4099651                    /usr/lib/libgmx.so.6
7fb120707000-7fb120708000 rw-p 00000000 00:00 0
7fb120708000-7fb1207f3000 r-xp 00000000 08:06 4099652                    /usr/lib/libmd.so.6
7fb1207f3000-7fb1209f3000 ---p 000eb000 08:06 4099652                    /usr/lib/libmd.so.6
7fb1209f3000-7fb1209f4000 r--p 000eb000 08:06 4099652                    /usr/lib/libmd.so.6
7fb1209f4000-7fb1209f5000 rw-p 000ec000 08:06 4099652                    /usr/lib/libmd.so.6
7fb1209f5000-7fb120baa000 r-xp 00000000 08:06 3014908                    /lib/x86_64-linux-gnu/libc-2.15.so
7fb120baa000-7fb120da9000 ---p 001b5000 08:06 3014908                    /lib/x86_64-linux-gnu/libc-2.15.so
7fb120da9000-7fb120dad000 r--p 001b4000 08:06 3014908                    /lib/x86_64-linux-gnu/libc-2.15.so
7fb120dad000-7fb120daf000 rw-p 001b8000 08:06 3014908                    /lib/x86_64-linux-gnu/libc-2.15.so
7fb120daf000-7fb120db4000 rw-p 00000000 00:00 0
7fb120db4000-7fb120f38000 r-xp 00000000 08:06 4099654                    /usr/lib/libgmxana.so.6
7fb120f38000-7fb121138000 ---p 00184000 08:06 4099654                    /usr/lib/libgmxana.so.6
7fb121138000-7fb121139000 r--p 00184000 08:06 4099654                    /usr/lib/libgmxana.so.6
7fb121139000-7fb121144000 rw-p 00185000 08:06 4099654                    /usr/lib/libgmxana.so.6
7fb121144000-7fb121146000 rw-p 00000000 00:00 0
7fb121146000-7fb121168000 r-xp 00000000 08:06 3014922                    /lib/x86_64-linux-gnu/ld-2.15.so
7fb121180000-7fb1211c5000 rw-p 00000000 00:00 0
7fb1211cd000-7fb1211ef000 rw-p 00000000 00:00 0
7fb1211ef000-7fb121288000 rw-p 00000000 00:00 0
7fb12129f000-7fb1212c1000 rw-p 00000000 00:00 0
7fb1212c1000-7fb121310000 rw-p 00000000 00:00 0
7fb12131d000-7fb121346000 rw-p 00000000 00:00 0
7fb121362000-7fb121368000 rw-p 00000000 00:00 0
7fb121368000-7fb121369000 r--p 00022000 08:06 3014922                    /lib/x86_64-linux-gnu/ld-2.15.so
7fb121369000-7fb12136b000 rw-p 00023000 08:06 3014922                    /lib/x86_64-linux-gnu/ld-2.15.so
7fff7be01000-7fff7be21000 rwxp 00000000 00:00 0                          [stack]
7fff7be21000-7fff7be22000 rw-p 00000000 00:00 0
7fff7bf39000-7fff7bf3a000 r-xp 00000000 00:00 0                          [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0                  [vsyscall]
Aborted (core dumped)

I reinstalled gromacs on my system, but the problem persists. Can somebody please help?

Thanks.