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param.txt
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>> DEBUG:
12-6 LJ parameters from [JPCC 2008,112,17281–17290] and [npj Comput Mater 7, 17 (2021)]
metal r0 epsilon A B
Ag 2.955 4.56 2021000 6072,
Al 2.925 4.02 1577000 5035,
Au 2.951 5.29 2307000 6987,
Cu 2.616 4.72 484800 3026,
Ni 2.552 5.65 431100 3121,
Pb 3.565 2.93 12350000 12030,
Pd 2.819 6.15 1549000 6173,
Pt 2.845 7.80 2193000 8272,
Ac 3.843 6.51 67550000 41940,
Ca 4.025 3.36 60750000 28570,
Ce 3.734 6.38 46870000 34590,
Es 4.133 2.88 71540000 28710,
Ir 2.785 9.20 2003000 8586,
Fe 2.590 6.00 546700 3620,
Rh 2.757 7.84 1512000 6886,
Sr 4.379 3.40 169000000 47950,
Th 3.683 8.47 52760000 42280,
Yb 3.942 2.71 38160000 20340
For amber/charmm/cvff/oplsaa forcefield of gromacs:
>> DEBUG:
This article 12-6 LJ form:
E = eps*[(r0/r)^12 - 2*(r0/r)^6]
Convert it to below form for gromacs:
E = 4*epsilon*[(sigma/r)^12 - (sigma/r)^6]
That is, sigma = r0 * 2^(-1/6)
#metal sigma(nm) epsilon(kJ/mol)
Ag 0.263260571 19.079040000
Al 0.260587875 16.819680000
Au 0.262904212 22.133360000
Cu 0.233059105 19.748480000
Ni 0.227357353 23.639600000
Pb 0.317605393 12.259120000
Pd 0.251144349 25.731600000
Pt 0.253460685 32.635200000
Ac 0.342372377 27.237840000
Ca 0.358586734 14.058240000
Ce 0.332661581 26.693920000
Es 0.368208440 12.049920000
Ir 0.248115293 38.492800000
Fe 0.230742768 25.104000000
Rh 0.245620777 32.802560000
Sr 0.390124549 14.225600000
Th 0.328117998 35.438480000
Yb 0.351192275 11.338640000
For gromos forcefield of gromacs:
#metal C6 C12
Ag 0.0254057 8.45758e-06
Al 0.021067 6.59672e-06
Au 0.0292343 9.65335e-06
Cu 0.0126587 2.02855e-06
Ni 0.0130603 1.80388e-06
Pb 0.0503323 5.16623e-05
Pd 0.0258266 6.48049e-06
Pt 0.0346107 9.17643e-06
Ac 0.175479 0.000282629
Ca 0.119552 0.000254168
Ce 0.144707 0.000196112
Es 0.120118 0.000299343
Ir 0.035922 8.38073e-06
Fe 0.0151555 2.28739e-06
Rh 0.028811 6.32629e-06
Sr 0.200609 0.000707245
Th 0.176895 0.000220747
Yb 0.0850924 0.000159647
append:
TiO2 12-6 LJ parameters from Journal of Chemical Physics, 2015, 142(23):2891-2959.
#elements sigma(nm) epsilon(kJ/mol)
TI 1.95998e-01 2.42672
O 2.88651e-01 1.29704