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 chargeptype sigma eps
HW 1 1.00800 0.4100A0.0e-01 0.0e-01
;clayFF_waterhydrogen
HO 1 1.00800 0.4250A0.0e-01 0.0e-01
;clayFF_hydroxylhydrogen
OW 8 15.99800-0.8200A3.16557e-01 6.50209e-01
;ClayFF_wateroxygen
OH 8 15.99800-0.9500A3.16557e-01 6.50209e-01
;ClayFF_hydroxyloxygen
OB 8 15.99800-1.0500A3.16557e-01 6.50209e-01
;ClayFF_bridgingoxygen
OBOS 8 15.99800-1.1808A3.16557e-01 6.50209e-01
;ClayFF_bridgingoxygenoctasub
OBTS 8 15.99800-1.1688A3.16557e-01 6.50209e-01
;ClayFF_bridgingoxygentetrsub
OHS 8 15.99800-1.0808A3.16557e-01 6.50209e-01
;ClayFF_hydroxyloxygensub
SI 14 28.08600 2.1000A3.30208e-01 8.0e-06
;ClayFF_tetrahedralsilicon
AO 13 26.98200 1.5750A4.27128e-01 6.0e-06
;ClayFF_octahedalaluminium
AT 13 26.98200 1.5750A3.30206e-01 8.0e-06
;ClayFF_tetrasubaluminium
ffbonded
[ bondtypes ]
; ij func b0 kb
OW HW 10.1000 554134.9
OH HO 10.1000 554134.9
OHSHO 10.1000 554134.9
[ angletypes ]
; ijk func th0 cth
HW OWHW1109.47191.564
AL OHHO1109.47125.52
atomtype.n2t
HHW0.4100 1.008 1O 0.100 ;water hydrogen
OOW -0.820015.998 2H 0.100H 0.100 ;water oxygen
OH2 OH -0.950015.998 1H 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 st2.100028.086 0 ;tetrahedral silicon
Al ao1.575026.982 0 ;octahedral aluminium
Mg mgo1.360024.305 0 ; octahedral magnisium
Na Na1.22.999 0 ;sodium ion
forcefield.doc
clayff.ff force field
forcefield.itp
#define _ff_clayff
[ defaults ]
; nbfunccomb-rule gen-pairs fudgeLJ fudgeQQ
1 3 yes 0.5 0.5
#include "ffnonbonded.itp"
#include "ffbonded.itp"
pdb
Al0.6494.3333.377
Al3.248.8053.377
Al3.2032.8513.362
Al0.6397.3243.362
Si4.9623.0160.65
Si2.3987.4880.65
Si2.4421.470.653
Si-0.1225.9420.653
O1-0.3343.0982.268
O12.2587.572.268
O10.0415.8392.271
O12.6051.3672.271
O30.0144.4720
O3-1.8854.2597.154
O35.1694.4720
O33.274.2597.154
O32.57800
O30.678-0.2147.154
O32.6058.9450
O30.7068.7317.154
O31.0342.0560.177
O33.6266.5290.177
O31.0526.8480.023
O33.6162.3760.023
OH1-0.3228.6062.304
OH12.2424.1332.304
OH23.831.364.329
OH21.2665.8324.329
OH2-0.9624.1364.35
OH21.6298.6084.35
OH2-0.9617.5354.36
OH21.6023.0634.36
O22.63310.3122.271
OH23.85810.3054.329
OH24.8348.6062.304
OH24.1947.5354.36
O34.8213.0982.268
OH34.1934.1364.35
O36.192.0560.177
O3-1.5296.5290.177
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==
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