[gmx-users] Reshaping of triclinic box
Dear all, I am running a simulation on gromacs 3.3 using periodic boundary conditions in a triclinic box with anisotropic pressure coupling. Since the simulation box has suffered some deformations, it is not rectangular anymore. 1- I would like to know if it is possible to apply some transformations to the actual coordinates in order to obtain again a rectangular box. 2- I would also like to set a new center for the simulation box. Thanks in advance Cesar ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Segmentation fault with gromacs 3.3.3
Once again, in reply to myself I could state that gromacs-3.3.3 won't build correctly on debian systems with gcc-4.3 neither. gmxtest simple dumps the following information. *** glibc detected *** mdrun: realloc(): invalid next size: 0x082a20d0 *** === Backtrace: = /lib/i686/cmov/libc.so.6[0xb7c0a673] /lib/i686/cmov/libc.so.6(realloc+0x10b)[0xb7c0c5cb] mdrun[0x8146fdd] === Memory map: 08048000-08283000 r-xp 08:05 1182361/usr/local/gromacs/bin/mdrun 08283000-0828a000 rwxp 0023b000 08:05 1182361/usr/local/gromacs/bin/mdrun 0828a000-082b rwxp 0828a000 00:00 0 [heap] b7a0-b7a21000 rwxp b7a0 00:00 0 b7a21000-b7b0 ---p b7a21000 00:00 0 b7b5c000-b7b5e000 rwxp b7b5c000 00:00 0 b7b5e000-b7b62000 r-xp 08:05 654102 /usr/lib/libXdmcp.so.6.0.0 b7b62000-b7b63000 rwxp 3000 08:05 654102 /usr/lib/libXdmcp.so.6.0.0 b7b63000-b7b65000 r-xp 08:05 656196 /usr/lib/libXau.so.6.0.0 b7b65000-b7b66000 rwxp 1000 08:05 656196 /usr/lib/libXau.so.6.0.0 b7b66000-b7b68000 r-xp 08:05 963745 /lib/i686/cmov/libdl-2.7.so b7b68000-b7b6a000 rwxp 1000 08:05 963745 /lib/i686/cmov/libdl-2.7.so b7b6a000-b7b81000 r-xp 08:05 653184 /usr/lib/libxcb.so.1.0.0 b7b81000-b7b82000 rwxp 00016000 08:05 653184 /usr/lib/libxcb.so.1.0.0 b7b82000-b7b83000 r-xp 08:05 653441 /usr/lib/libxcb-xlib.so.0.0.0 b7b83000-b7b84000 rwxp 08:05 653441 /usr/lib/libxcb-xlib.so.0.0.0 b7b84000-b7b85000 rwxp b7b84000 00:00 0 b7b85000-b7b99000 r-xp 08:05 963756 /lib/i686/cmov/libpthread-2.7.so b7b99000-b7b9b000 rwxp 00013000 08:05 963756 /lib/i686/cmov/libpthread-2.7.so b7b9b000-b7b9d000 rwxp b7b9b000 00:00 0 b7b9d000-b7ce5000 r-xp 08:05 963742 /lib/i686/cmov/libc-2.7.so b7ce5000-b7ce6000 r-xp 00148000 08:05 963742 /lib/i686/cmov/libc-2.7.so b7ce6000-b7ce8000 rwxp 00149000 08:05 963742 /lib/i686/cmov/libc-2.7.so b7ce8000-b7ceb000 rwxp b7ce8000 00:00 0 b7ceb000-b7dd6000 r-xp 08:05 219962 /usr/lib/libX11.so.6.2.0 b7dd6000-b7dd9000 rwxp 000eb000 08:05 219962 /usr/lib/libX11.so.6.2.0 b7dd9000-b7dda000 rwxp b7dd9000 00:00 0 b7dda000-b7dee000 r-xp 08:05 654098 /usr/lib/libICE.so.6.3.0 b7dee000-b7def000 rwxp 00014000 08:05 654098 /usr/lib/libICE.so.6.3.0 b7def000-b7df1000 rwxp b7def000 00:00 0 b7df1000-b7df8000 r-xp 08:05 656152 /usr/lib/libSM.so.6.0.0 b7df8000-b7df9000 rwxp 6000 08:05 656152 /usr/lib/libSM.so.6.0.0 b7df9000-b7e1c000 r-xp 08:05 963746 /lib/i686/cmov/libm-2.7.so b7e1c000-b7e1e000 rwxp 00023000 08:05 963746 /lib/i686/cmov/libm-2.7.so b7e1e000-b7e1f000 rwxp b7e1e000 00:00 0 b7e1f000-b7efc000 r-xp 08:05 652016 /usr/lib/libfftw3f.so.3.1.2 b7efc000-b7f02000 rwxp 000dd000 08:05 652016 /usr/lib/libfftw3f.so.3.1.2 b7f02000-b7f16000 r-xp 08:05 963748 /lib/i686/cmov/libnsl-2.7.so b7f16000-b7f18000 rwxp 00013000 08:05 963748 /lib/i686/cmov/libnsl-2.7.so b7f18000-b7f1a000 rwxp b7f18000 00:00 0 b7f1d000-b7f29000 r-xp 08:05 676535 /lib/libgcc_s.so.1 b7f29000-b7f2a000 rwxp b000 08:05 676535 /lib/libgcc_s.so.1 b7f2a000-b7f2d000 rwxp b7f2a000 00:00 0 b7f2d000-b7f47000 r-xp 08:05 677881 /lib/ld-2.7.so b7f47000-b7f49000 rwxp 00019000 08:05 677881 /lib/ld-2.7.so bf985000-bf99c000 rwxp bffe9000 00:00 0 [stack] e000-f000 r-xp 00:00 0 [vdso] sh: line 1: 6267 Abortadomdrun mdrun.out 21 FAILED. Check files in rb1 1 out of 16 simple tests FAILED On the other hand, mpi version of gromacs built on the same system, succesfully passes all simple test. Cesar Avila escribió: It seems to be a problem related to the debian package. I have compiled gromacs 3.3.3 from source with gcc-4.3 and apparently the problem has dissapeared. Perhaps, the binaries on the debian package were compiled with gcc-4.1. Cesar Avila escribió: Dear all, I am new to the gromacs simulation package. Thus far I have been using Charmm and NAMD, but now I am interested on testing Marrink's Coarse-Grained Martini FF. I managed to setup an initial configuration for a protein in a water box. After a few minimization steps, I ran the simulation for about 10 ns until it crashed with a Segmentation fault message. Using tpbconv, I resumed the simulation from 10200 ps step. Nevertheless I systematically found a segmentation fault error on step 6530. Using mdrun -nocompact gives no additional information about the crash. When I use mdrun -debug the simulation is able to run without any problem (until I run out of disk space). I found the same error to occur on both a Pentium IV (debian etch) and an Intel Core 2 Duo (Debian lenny). Both systems are running gromacs 3.3.3 from Debian testing packages. If anyone is interested on reproducing the error on their own computer, I can send them the tpr file (476K compressed
[gmx-users] tpbconv functionality
I found the tpbconv tool very usefull for generating tpr files for resuming the simulations. Nevertheless I couldn't find an option to set/change the number of processors to use as the -np option in grompp. Is there a way to do this? ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Segmentation fault with gromacs 3.3.3
Dear all, I am new to the gromacs simulation package. Thus far I have been using Charmm and NAMD, but now I am interested on testing Marrink's Coarse-Grained Martini FF. I managed to setup an initial configuration for a protein in a water box. After a few minimization steps, I ran the simulation for about 10 ns until it crashed with a Segmentation fault message. Using tpbconv, I resumed the simulation from 10200 ps step. Nevertheless I systematically found a segmentation fault error on step 6530. Using mdrun -nocompact gives no additional information about the crash. When I use mdrun -debug the simulation is able to run without any problem (until I run out of disk space). I found the same error to occur on both a Pentium IV (debian etch) and an Intel Core 2 Duo (Debian lenny). Both systems are running gromacs 3.3.3 from Debian testing packages. If anyone is interested on reproducing the error on their own computer, I can send them the tpr file (476K compressed). Best regards Cesar Avila Universidad Nacional de Tucuman. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Segmentation fault with gromacs 3.3.3
It seems to be a problem related to the debian package. I have compiled gromacs 3.3.3 from source with gcc-4.3 and apparently the problem has dissapeared. Perhaps, the binaries on the debian package were compiled with gcc-4.1. Cesar Avila escribió: Dear all, I am new to the gromacs simulation package. Thus far I have been using Charmm and NAMD, but now I am interested on testing Marrink's Coarse-Grained Martini FF. I managed to setup an initial configuration for a protein in a water box. After a few minimization steps, I ran the simulation for about 10 ns until it crashed with a Segmentation fault message. Using tpbconv, I resumed the simulation from 10200 ps step. Nevertheless I systematically found a segmentation fault error on step 6530. Using mdrun -nocompact gives no additional information about the crash. When I use mdrun -debug the simulation is able to run without any problem (until I run out of disk space). I found the same error to occur on both a Pentium IV (debian etch) and an Intel Core 2 Duo (Debian lenny). Both systems are running gromacs 3.3.3 from Debian testing packages. If anyone is interested on reproducing the error on their own computer, I can send them the tpr file (476K compressed). Best regards Cesar Avila Universidad Nacional de Tucuman. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
