Dongsheng Zhang wrote:
Dear GMX users:
Could someone help me to understand these information from a position
restrained tpr file?
1. excl[0][0..17]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 13, 14, 15,
16, 18, 26, 28}
Exclusion group 0, there are total 17 exclusions in this group. between
0 (the first one) and remaining 17 atoms.
2. blocks[CGS][0][0..19]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11,
12, 13, 14, 15, 16, 17, 18, 19}
3. blocks[MOLS][2][1802..1805]={1802, 1803, 1804, 1805}
Both are useful for dividing the atoms for parallel processing (before
domain decomposition arrives in gmx 4.0 :-).
CGS means charge group. MOLS means molecules. Division shall not break
one charge group or a molecule (hope that I am not wrong here).
4. blocks[SBLOCKS][0][0..1039]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9,
10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23,
24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37,
38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51,
52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64,
65, ........... 1039}
Not sure...
5. functype[0]=LJ_SR, c6= 5.72640402e-03, c12= 1.86486031e-05
I know this is for the parameters of LJ potential. My question is where
is the information that tells gromacs to use these parameters for the
interaction between two specific atoms.
see atoms: section; type there refers to the functype here. Any functype
number for LJ_SR beyond the atom number there will not be used.
As someone has suggested, if gromacs website can offer the
interpretation for each file, I believe many people will highly
appreciate it.
All the best!
Dongsheng
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