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gmx_rescue_LFShot!

09.09.2005

Oliver Beckstein added Large File Support to this program. This is a utility to rescue partly corrupted XTC files. It works under Linux and is based on earlier files contributed for SGI (see README.rescue) The actual files are called gmx_rescue.c and README.rescue. It came in handy for me because a lot of simulations that I had run on some supercomputer had corrupted XTC files (apparently due to hardware problems or NFS errors). Rescuing them made me (up to now) just loose about 10 frames in 2500, so I think this is still acceptable and avoids re-running the simulations.
Uploaded 12:16 September 12, 2004 by Marc Baaden (baaden at smplinux.de)

gmx_rescuehot!

09.09.2005

This is a utility to rescue partly corrupted XTC files. It works under Linux and is based on earlier files contributed for SGI (see README.rescue) The actual files are called gmx_rescue.c and README.rescue. It came in handy for me because a lot of simulations that I had run on some supercomputer had corrupted XTC files (apparently due to hardware problems or NFS errors). Rescuing them made me (up to now) just loose about 10 frames in 2500, so I think this is still acceptable and avoids re-running the simulations.
Uploaded 23:02 August 16, 2004 by Marc Baaden (baaden at smplinux.de)

gmx_alltoallhot!

21.07.2006

This contribution is for GROMACS users who experience poor parallel scaling with PME on Ethernet connected clusters. It consists of
1.) a program to test if there are TCP packet drops during MPI_Alltoall communication on your cluster
2.) a patch for gromacs 3.3.1 that incorporates an optimised all-to-all algorithm to reduce packet loss

genbox-maxsol-patchhot!

29.05.2008

This is a patch to addconf.c, in the tools directory, which improves the --maxsol option to genbox (which limits the number of solvent molecules added). The maxsol option works by removing some of the solvent molecules that have already been added; this patch targets solvent molecules that are at the edges of the box to be removed first. It applies to GROMACS 3.3.2, and probably to 3.3.3, but I have not tested this yet.

Homepage: http://cesario.rutgers.edu/easmith/research/

FFTW for Solaris x86_64 (Double precision)hot!

14.12.2007

GROMACS compiled for Solaris 10 using Sun Studio 12 compiler for X86_64 (AMD Opteron) processors.

Compiled with flag : -fast

Configured with flag : --enable-shared --enable-threads

For any questions regarding the por, contact Mithun Sridharan (Mithun.Sridharan@Sun.COM or mithun@sun.com)

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