Mercurial > repos > chemteam > gromacs_extract_topology
view test-data/water_bondedparams.itp @ 0:9faa4f4b8b76 draft default tip
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tree/master/tools/buildtools/topologyeditors commit ae026d4ea6fe2ebaa53611b86f9047941c7b899b"
author | chemteam |
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date | Thu, 27 Jan 2022 18:17:05 +0000 |
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; ; Horn et al. (2004). J. Chem. Phys.120, 9665-9678 ; [ moleculetype ] ; molname nrexcl SOL 2 [ atoms ] ; id at type res nr res name at name cg nr charge mass 1 OW_tip4pew 1 SOL OW 1 0 16.00000 2 HW_tip4pew 1 SOL HW1 1 0.52422 1.00800 3 HW_tip4pew 1 SOL HW2 1 0.52422 1.00800 4 MW 1 SOL MW 1 -1.04844 0.00000 #ifndef FLEXIBLE [ settles ] ; i funct doh dhh 1 1 0.09572 0.15139 #else [ bonds ] ; i j funct length force.c. 1 2 1 0.09572 502416.0 0.09572 502416.0 1 3 1 0.09572 502416.0 0.09572 502416.0 [ angles ] ; i j k funct angle force.c. 2 1 3 1 104.52 628.02 104.52 628.02 #endif [ virtual_sites3 ] ; Vsite from funct a b 4 1 2 3 1 0.106676721 0.106676721 [ 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: ; ; O ; ; V ; ; H H ; ; Ewald tip4p: ; const = distance (OV) / [ cos (angle(VOH)) * distance (OH) ] ; 0.0125 nm / [ cos (52.26 deg) * 0.09572 nm ] ; then a = b = 0.5 * const = 0.106676721 ; ; Vsite pos x4 = x1 + a*(x2-x1) + b*(x3-x1)