Dongsheng Zhang wrote:
Yang Ye,
Thank you very much for your help. I still have some questions:
On Mon, 2006-07-10 at 11:35 +0800, Yang Ye wrote:
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.
Is this exclusion for nonbonded interactions, including 1-2, 1-3
interactions? If so, I don't understand why there are 17 atoms to be
excluded for atom 0. It is a capped carbon nanotube. Each C has three
single covalent bond, so the total exluded atoms for each atom should be
6.
This is next term for exlusion:
excl[1][18..35]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12,
13, 14, 15, 20, 22}
Why are there two different exclusions for atom 0?
Please check your top file, including those files included into it.
Remove/Change some and compare the dump.
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...
Anyone can help me for this one? Thanks!
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.
I am sorry I am not clear here. I know C6 and C12 is for the LJ
interaction between C and C in nanotube by looking at **nb.itp file. How
can gromacs know it in tpr file (I believe all information should be in
tpr file)? Let me give you an example. In tpr file, type=81 (ANGLES)
1041 1040 1042 shows that the angle bending parameters for atoms 1041
1040 1042 are from functype[81], but I can't find any information which
says the LJ parameters for C and C are from functype[0].
mdrun will associate functype[i] with atom type. check gmx source code
if you are still not sure.
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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