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DocumentsDate added
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Gromacs Topology toolshot!
- 09.09.2005
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nr2nametop replaces the atom numbers in your topology with atom name labels.
renumtop renumbers all atom numbers (or replaces labels by numbers) in your topology.
nr2nametop can be used to convert an .itp file into an .rtp entry. renumtop can be used to manually add or remove atoms from a topology and even to merge two topologies. Using nr2nametop can be helpful to tweak your molecules parameters because when defining e.g. a bond you see which atoms it connects. renumtop will change the labels back to numbers.
Finally, process_top writes out a topology with all parameters and atom names explicit, for example to be used as a table in a publication.
Uploaded 09:40 July 27, 2004 by Anton Feenstra (feenstra at few.vu.nl) - Hits: 2540
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Gromacs 3.3.1 64-bit/32-bit native Windows port with Assembly Loops and MPI supporthot!
- 08.10.2007
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Features:
1. Provides support for parallel (MPI) version.
2. Makes use of assembly loops to improve the performance.
3. Supports both 64-bit and 32-bit Windows platforms.
4. Provides support for Visual Studio 2005 IDE build as well as
command-line build (using nmake utility).
5. Can be built in single or double precision mode.
6. Can be configured to use Intel Math Kernel Library (IMKL).
7. Can be built in Release or Debug mode.
8. IDE build mechanism supports batch build.
9. Gromacs binaries/libraries can co-exist for single/double precision,
debug/release mode, normal/parallel (MPI) version, default/IMKL libraries
and for 64-bit/32-bit platforms.
10. Windows port does not modify the existing source code; it just adds the
Windows specific code using the compiler preprocessor directives.Please refer the readme-windows.txt and
"Migration of Gromacs 3.3.1 on Microsoft Windows.doc" files shipped with this
package for more details. - Hits: 1490
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Gromacs 3.2 with PVM supporthot!
- 12.09.2005
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This version of Gromacs 3.2 supports PVM 3.4.4 for parallel computation. It was
tested on a RedHat 7.2 Linux cluster, with 2.7% of total computation time gain
on the MPI version.
Uploaded 16:08 February 17, 2004 by Marco Maniezzo (marco.maniezzo@polito.it) - Hits: 1891
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gridcount-1.0hot!
- 09.09.2005
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g_ri3Dc grid-counts atoms or molecules from an index file and writes a 3D density file (portable xdr format). The analysis tool a_ri3Dc reads the 3D density and can convert it into gOpenMols plt format (can be imported into VMD), ascii dump, or it can do 2D slices (in xfarbe format) or cylindrical averages (see these examples), useful for looking at ion channels. See the README and INSTALL for compilation instructions. gricount 1.0 is (1) GPL, (2) can be compiled in the Gromacs source tree or standalone.
Uploaded 17:30 March 23, 2004 by Oliver Beckstein (oliver@biop.ox.ac.uk) - Hits: 2194
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gridcounthot!
- 09.09.2005
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g_ri3Dc grid-counts atoms or molecules from an index file and writes a 3D density file (portable xdr format). The analysis tool a_ri3Dc reads the 3D density and can convert it into gOpenMol\'s plt format (can be imported into VMD), ascii dump, or it can do 2D slices (in xfarbe format) or cylindrical averages (see these examples), useful for looking at ion channels. See the README for compilation instructions (tested with Gromacs 3.1.4 and 3.2.1).
Uploaded 01:51 March 18, 2004 by Oliver Beckstein - Hits: 1598
