[gmx-users] Could not find clayff forcefield
Justin Lemkul
jalemkul at vt.edu
Sun Aug 6 02:36:30 CEST 2017
On 8/4/17 4:57 AM, G R wrote:
> Dear users,
>
> I try to implement Clayff forcefield for Kaolinite. I created my force
> field (I'm not sure about it), but gromacs couldn't find my force field in
> the directory. Here is my forcefield.
>
> ffnonbonded
> [ atomtypes ]
> ; name mass charge ptype sigma eps
> HW 1 1.00800 0.4100 A 0.00000e-01 0.00000e-01
> ;clayFF_waterhydrogen
> HO 1 1.00800 0.4250 A 0.00000e-01 0.00000e-01
> ;clayFF_hydroxylhydrogen
> OW 8 15.99800 -0.8200 A 3.16557e-01 6.50209e-01
> ;ClayFF_wateroxygen
> OH 8 15.99800 -0.9500 A 3.16557e-01 6.50209e-01
> ;ClayFF_hydroxyloxygen
> OB 8 15.99800 -1.0500 A 3.16557e-01 6.50209e-01
> ;ClayFF_bridgingoxygen
> OBOS 8 15.99800 -1.1808 A 3.16557e-01 6.50209e-01
> ;ClayFF_bridgingoxygenoctasub
> OBTS 8 15.99800 -1.1688 A 3.16557e-01 6.50209e-01
> ;ClayFF_bridgingoxygentetrsub
> OHS 8 15.99800 -1.0808 A 3.16557e-01 6.50209e-01
> ;ClayFF_hydroxyloxygensub
> SI 14 28.08600 2.1000 A 3.30208e-01 8.0e-06
> ;ClayFF_tetrahedralsilicon
> AO 13 26.98200 1.5750 A 4.27128e-01 6.0e-06
> ;ClayFF_octahedalaluminium
> AT 13 26.98200 1.5750 A 3.30206e-01 8.0e-06
> ;ClayFF_tetrasubaluminium
>
> ffbonded
> [ bondtypes ]
> ; i j func b0 kb
> OW HW 1 0.1000 554134.9
> OH HO 1 0.1000 554134.9
> OHS HO 1 0.1000 554134.9
>
> [ angletypes ]
> ; i j k func th0 cth
> HW OW HW 1 109.47 191.5000064
> AL OH HO 1 109.47 125.52
>
> atomtype.n2t
> H HW 0.4100 1.008 1 O 0.100 ;water hydrogen
> O OW -0.8200 15.998 2 H 0.100 H 0.100 ;water oxygen
> OH2 OH -0.9500 15.998 1 H 0.100 ;hydroxyl oxygen
> O2 obts -1.1688 15.998 0 ;bridging oxygen with
> tetrahedral substitution
> O1 obss -1.2996 15.998 0 ;bridging oxygen with
> double substitution
> OH1 ohs -1.0808 15.998 1 H 0.100 ;hydroxyl hydrogen with
> substitution
> Si st 2.1000 28.086 0 ;tetrahedral silicon
> Al ao 1.5750 26.982 0 ;octahedral aluminium
> Mg mgo 1.3600 24.305 0 ; octahedral magnisium
> Na Na 1.0000 22.999 0 ;sodium ion
>
> forcefield.doc
> clayff.ff force field
>
> forcefield.itp
> #define _ff_clayff
>
>
> [ defaults ]
> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
> 1 3 yes 0.5 0.5
>
> #include "ffnonbonded.itp"
> #include "ffbonded.itp"
>
> pdb
>
> Al 0.649 4.333 3.377
> Al 3.24 8.805 3.377
> Al 3.203 2.851 3.362
> Al 0.639 7.324 3.362
> Si 4.962 3.016 0.65
> Si 2.398 7.488 0.65
> Si 2.442 1.47 0.653
> Si -0.122 5.942 0.653
> O1 -0.334 3.098 2.268
> O1 2.258 7.57 2.268
> O1 0.041 5.839 2.271
> O1 2.605 1.367 2.271
> O3 0.014 4.472 0
> O3 -1.885 4.259 7.154
> O3 5.169 4.472 0
> O3 3.27 4.259 7.154
> O3 2.578 0 0
> O3 0.678 -0.214 7.154
> O3 2.605 8.945 0
> O3 0.706 8.731 7.154
> O3 1.034 2.056 0.177
> O3 3.626 6.529 0.177
> O3 1.052 6.848 0.023
> O3 3.616 2.376 0.023
> OH1 -0.322 8.606 2.304
> OH1 2.242 4.133 2.304
> OH2 3.83 1.36 4.329
> OH2 1.266 5.832 4.329
> OH2 -0.962 4.136 4.35
> OH2 1.629 8.608 4.35
> OH2 -0.961 7.535 4.36
> OH2 1.602 3.063 4.36
> O2 2.633 10.312 2.271
> OH2 3.858 10.305 4.329
> OH2 4.834 8.606 2.304
> OH2 4.194 7.535 4.36
> O3 4.821 3.098 2.268
> OH3 4.193 4.136 4.35
> O3 6.19 2.056 0.177
> O3 -1.529 6.529 0.177
>
>
> It's to long, Sorry about it, but I really need to find out where is my
> problem. I put n2t file in directory not in my forcefield subdirectory. Do
That's wrong. It needs to be in the force field subdirectory.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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