Hi All Thanks to Christopher Neale for his comments. There was a frame missing. But the frame was nowhere near the end. I played around with the trajectory and timestamps, got rid of that frame and obtained the density. Interestingly, g_density in version 4.5.4 was able to run the .xtc. It mentioned that there was a frame missing, but it gave me the right output.
On Fri, Mar 8, 2013 at 9:25 PM, Christopher Neale [via GROMACS] < ml-node+s5086n5006228...@n6.nabble.com> wrote: > 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. > -- > gmx-users mailing list [hidden > email]<http://user/SendEmail.jtp?type=node&node=5006228&i=0> > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [hidden > email]<http://user/SendEmail.jtp?type=node&node=5006228&i=1>. > > * Can't post? 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