Dear GROMACS users,
I'm wondering how can I correctly describe H-H radial distribution function of heavy water.
Please check atteched file HH_rdf.PNG which is a calculated result of H-H radial distribution from my simulation.
The first peak is due to the intramolecular interaction of water molecules.
It shows almolst 7 at 0.13 nm but when comparing this result with an experimental data, the experimental data shows just almost 2 at the first peak.
I have tried many times of simulations but i couldn't find why this huge difference is caused.
I used tip4p/2005f water model and used potential is atteched below.
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 3 yes 0.5 0.5
[ moleculetype ]
; molname nrexcl
SOL 2
[ atoms ]
; id at type res nr residu name at name cg nr charge
1 opls_113 1 SOL OW 1 0.0
2 opls_114 1 SOL HW1 1 0.5564
3 opls_114 1 SOL HW2 1 0.5564
4 opls_115 1 SOL MW 1 -1.1128
;[nonbond_params]
; i j funct q V W
;1 2 1 0.5564 3.16440e-01 7.74907e-01
;1 3 1 0.5564 3.16440e-01 7.74907e-01
#ifndef FLEXIBLE
[ settles ]
; OW funct doh dhh
1 1 0.09664 0.15555
#else
[ bonds ]
; i j funct length D beta
1 2 3 0.09419 432.581 22.87 ; For TIP4P/2005f Water b0, D, beta
1 3 3 0.09419 432.581 22.87 ; For TIP4P/2005f Water b0, D, beta
[ angles ]
; i j k funct angle force.c.
2 1 3 1 107.4 367.81
#endif
[ exclusions ]
1 2 3 4
2 1 3 4
3 1 2 4
4 1 2 3
; The position of the virtual site is computed as follows:
;
; const = distance (OD) / [ cos (angle(DOH)) * distance (OH) ]
; 0.015 nm / [ cos (52.26 deg) * 0.09572 nm ]
; Vsite pos x4 = x1 + a*(x2-x1) + b*(x3-x1)
[ virtual_sites3 ]
; Vsite from funct a b
4 1 2 3 1 0.13288 0.13288
I used -DFLEXIBLE option and energy minimization, NVT, NPT equlibration and NVE production run.
If someone would find some wrong things, please let me know.
Thank you.
Haelee Hyun
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