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 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.