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Date |
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#Lines |
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| .. | | 21-Aug-2017 | - |
| moldb/ | H | 21-Dec-2006 | - | 1,381 | 1,376 |
| test1/ | H | 12-Jun-2008 | - | 16,909 | 16,904 |
| test2/ | H | 21-Dec-2006 | - | 19,719 | 19,713 |
| test3/ | H | 01-Feb-2010 | - | 42 | 40 |
| README | H A D | 21-Dec-2006 | 1.1 KiB | 48 | 36 |
README
1MDynaMix Benchmarks
2-------------------
3Molecular dynamics simulations using MDynaMix package
4(http://www.fos.su.se/physical/sasha/md_prog.html)
5
63 tests, each in directory test1, test2, test3 are prepared
7The simulated systems are:
8
9test1
10-----
11This test run 1000 MD steps (2ps)
12for 128 united atom DMPC lipids and 3655 water molecules.
13GROMAS force field
14Constraint dynamics
1516853 atoms
16
17test2
18-----
19This test run 1000 MD steps (2ps)
20for 98 all atom DMPC lipids and 2700 water molecules.
21modified CHARMM force field
22flexible molecules; double time step
2319664 atoms
24
25test3
26-----
27This test run 50000 MD steps (100ps)
28for 256 flexible SPC water molecules.
29double time step
30
31Note: constraint dynamics is expected to show a better scaling
32
33Program code and compilation
34----------------------------
35
36The program code is in MDynaMix directory.
37There are 3 Makefiles, one of them Makefile.mpi is for parallel calculations
38Proper compiler optimization options should be set
39The executable is "mdp".
40Copy into one of test directory and run:
41
42mpirun -np 16 mdp > file.out
43
44(input is in "md.input" file)
45
46Information about CPU time is closer to the end of the output file.
47
48