| 1 | ! **************************************************************
|
|---|
| 2 | !
|
|---|
| 3 | ! This file contains the subroutines: opereg,gdtgbl,gdtreg
|
|---|
| 4 | !
|
|---|
| 5 | ! Copyright 2003-2005 Frank Eisenmenger, U.H.E. Hansmann,
|
|---|
| 6 | ! Shura Hayryan, Chin-Ku
|
|---|
| 7 | ! Copyright 2007 Frank Eisenmenger, U.H.E. Hansmann,
|
|---|
| 8 | ! Jan H. Meinke, Sandipan Mohanty
|
|---|
| 9 | !
|
|---|
| 10 | ! **************************************************************
|
|---|
| 11 |
|
|---|
| 12 | subroutine opereg(nml)
|
|---|
| 13 |
|
|---|
| 14 | ! .......................................................................
|
|---|
| 15 | ! PURPOSE: calculate regul. energy & it's partial derivatives
|
|---|
| 16 | ! for molecule 'nml' vs. variables 'iv'
|
|---|
| 17 | !
|
|---|
| 18 | ! NB: if the unit axis for an internal variable coincides with a
|
|---|
| 19 | ! global axis (i.e. for torsion or bond length variation round
|
|---|
| 20 | ! or along 'xrfax', respectively, and bd. angle var. round
|
|---|
| 21 | ! 'zrfax'): VdW & 14 interaction partners of moving set atoms
|
|---|
| 22 | ! should be used for calculation, instead of the mov. sets,
|
|---|
| 23 | ! with opposite sign.
|
|---|
| 24 | !
|
|---|
| 25 | ! Example: By the the way the molecule-fixed system is set up,
|
|---|
| 26 | ! changes in Phi_1 affect atomic positions BEFORE the
|
|---|
| 27 | ! N-C^alpha bond relatively to the space-fixed system,
|
|---|
| 28 | ! not the moving set of Phi_1.
|
|---|
| 29 | !
|
|---|
| 30 | ! CALLS: gdtgbl, gdtreg
|
|---|
| 31 | ! ......................................................................
|
|---|
| 32 |
|
|---|
| 33 | include 'INCL.H'
|
|---|
| 34 | include 'INCP.H'
|
|---|
| 35 |
|
|---|
| 36 | double precision xfvr, yfvr, zfvr, xfrvr, yfrvr, zfrvr, x1, y1, z1
|
|---|
| 37 | double precision a, sa, ca, xk, yk, zk, xi, yi, zi, xji, yji, zji
|
|---|
| 38 | double precision dx, dy, dz, x, y, z, xfat, yfat, zfat, xfrat
|
|---|
| 39 | double precision yfrat, zfrat, xb, yb, zb, ex, ey, ez, xfiv, yfiv
|
|---|
| 40 | double precision zfiv, xfriv, yfriv, zfriv
|
|---|
| 41 |
|
|---|
| 42 | integer ntlvr, nml, ix2, ifivr, ilavr, i, ii, j, i1s, i1a, io, iv
|
|---|
| 43 | integer it, ia, ib, i2s, ims, i1, i2, i2a, iad, lad, ivw, i14
|
|---|
| 44 |
|
|---|
| 45 | dimension xfat(mxat),yfat(mxat),zfat(mxat),
|
|---|
| 46 | & xfrat(mxat),yfrat(mxat),zfrat(mxat),
|
|---|
| 47 |
|
|---|
| 48 | & xfvr(mxvr),yfvr(mxvr),zfvr(mxvr),
|
|---|
| 49 | & xfrvr(mxvr),yfrvr(mxvr),zfrvr(mxvr)
|
|---|
| 50 |
|
|---|
| 51 | logical lnb
|
|---|
| 52 |
|
|---|
| 53 |
|
|---|
| 54 | ntlvr=nvrml(nml)
|
|---|
| 55 | if (ntlvr.eq.0) then
|
|---|
| 56 | write (logString, '(a,i4)')
|
|---|
| 57 | & ' opereg> No variables defined in molecule #',nml
|
|---|
| 58 | return
|
|---|
| 59 | endif
|
|---|
| 60 |
|
|---|
| 61 | ix2=ixrfpt(2,nml) ! as indicator for situation noted above
|
|---|
| 62 |
|
|---|
| 63 | ifivr=ivrml1(nml) ! 1st var. &
|
|---|
| 64 | ilavr=ifivr+ntlvr-1 ! last var. of 'nml'
|
|---|
| 65 |
|
|---|
| 66 | ! --------------------------- initializations
|
|---|
| 67 | do i=ifivr,ilavr
|
|---|
| 68 | gdeyrg(i)=0.d0
|
|---|
| 69 | xfvr(i)=0.d0
|
|---|
| 70 | yfvr(i)=0.d0
|
|---|
| 71 | zfvr(i)=0.d0
|
|---|
| 72 | xfrvr(i)=0.d0
|
|---|
| 73 | yfrvr(i)=0.d0
|
|---|
| 74 | zfrvr(i)=0.d0
|
|---|
| 75 | enddo
|
|---|
| 76 |
|
|---|
| 77 | ii=(nml-1)*6
|
|---|
| 78 |
|
|---|
| 79 | do i=ii+1,ii+6
|
|---|
| 80 | gdeygb(i) = 0.d0
|
|---|
| 81 | enddo
|
|---|
| 82 |
|
|---|
| 83 | x1=rfpt(1,nml) ! r_1
|
|---|
| 84 | y1=rfpt(2,nml)
|
|---|
| 85 | z1=rfpt(3,nml)
|
|---|
| 86 |
|
|---|
| 87 | a= gbpr(4,nml) ! alpha
|
|---|
| 88 | sa = sin(a)
|
|---|
| 89 | ca = cos(a)
|
|---|
| 90 |
|
|---|
| 91 | xk = yrfax(1,nml) ! axis K
|
|---|
| 92 | yk = yrfax(2,nml)
|
|---|
| 93 | zk = yrfax(3,nml)
|
|---|
| 94 |
|
|---|
| 95 | eyrg = 0.d0
|
|---|
| 96 |
|
|---|
| 97 | do i=iatrs1(irsml1(nml)),iatrs2(irsml2(nml))
|
|---|
| 98 |
|
|---|
| 99 | j = ixatp(i)
|
|---|
| 100 | if (j.gt.0) then
|
|---|
| 101 |
|
|---|
| 102 | xi = xat(i) ! position of atom in internal model
|
|---|
| 103 | yi = yat(i)
|
|---|
| 104 | zi = zat(i)
|
|---|
| 105 |
|
|---|
| 106 | xji = xatp(j) - xi ! x distance between internal model and PDB
|
|---|
| 107 | yji = yatp(j) - yi
|
|---|
| 108 | zji = zatp(j) - zi
|
|---|
| 109 |
|
|---|
| 110 | eyrg = eyrg + xji**2 + yji**2 + zji**2 ! The regularization energy is just
|
|---|
| 111 | ! the sum over the atom distances
|
|---|
| 112 | ! squared.
|
|---|
| 113 |
|
|---|
| 114 | dx = 2.d0 * xji ! f = - dE/dR_i
|
|---|
| 115 | dy = 2.d0 * yji ! The factor of 2 comes from the derivative
|
|---|
| 116 | dz = 2.d0 * zji
|
|---|
| 117 |
|
|---|
| 118 | ! =============================================== global pars.
|
|---|
| 119 |
|
|---|
| 120 | gdeygb(ii+1) = gdeygb(ii+1) - dx ! d(E_ij) / d(x_i)
|
|---|
| 121 | gdeygb(ii+2) = gdeygb(ii+2) - dy ! d(E_ij) / d(y_i)
|
|---|
| 122 | gdeygb(ii+3) = gdeygb(ii+3) - dz ! d(E_ij) / d(z_i)
|
|---|
| 123 |
|
|---|
| 124 | ! -------------------------- r = r_i - r_1
|
|---|
| 125 | x = xi - x1
|
|---|
| 126 | y = yi - y1
|
|---|
| 127 | z = zi - z1
|
|---|
| 128 |
|
|---|
| 129 | gdeygb(ii+4) = gdeygb(ii+4) +dx*y-dy*x ! d(E_ij) / d(a)
|
|---|
| 130 |
|
|---|
| 131 | gdeygb(ii+5) = gdeygb(ii+5) +z*(dy*ca-dx*sa)+dz*(x*sa-y*ca) ! d(E_ij) / d(b)
|
|---|
| 132 |
|
|---|
| 133 | gdeygb(ii+6) = gdeygb(ii+6) +dx*(zk*y-yk*z)+dy*(xk*z-zk*x) ! d(E_ij) / d(g)
|
|---|
| 134 | & +dz*(yk*x-xk*y)
|
|---|
| 135 |
|
|---|
| 136 | ! =============================================== for internal vars.
|
|---|
| 137 |
|
|---|
| 138 | xfat(i) = dx
|
|---|
| 139 | yfat(i) = dy
|
|---|
| 140 | zfat(i) = dz
|
|---|
| 141 |
|
|---|
| 142 | xfrat(i) = dy*zi-dz*yi ! g = f x r
|
|---|
| 143 | yfrat(i) = dz*xi-dx*zi !
|
|---|
| 144 | zfrat(i) = dx*yi-dy*xi !
|
|---|
| 145 |
|
|---|
| 146 | else
|
|---|
| 147 | xfat(i) = 0.d0
|
|---|
| 148 | yfat(i) = 0.d0
|
|---|
| 149 | zfat(i) = 0.d0
|
|---|
| 150 | xfrat(i) = 0.d0
|
|---|
| 151 | yfrat(i) = 0.d0
|
|---|
| 152 | zfrat(i) = 0.d0
|
|---|
| 153 | endif
|
|---|
| 154 |
|
|---|
| 155 | enddo ! atoms
|
|---|
| 156 |
|
|---|
| 157 | if (tesgrd) call gdtgbl(nml)
|
|---|
| 158 |
|
|---|
| 159 | i1s=imsml1(nml)+nmsml(nml) ! last mov. set of 'nml' + 1
|
|---|
| 160 | i1a=iadml1(nml)+nadml(nml) ! last added var. of 'nml' + 1
|
|---|
| 161 |
|
|---|
| 162 | do io=ilavr,ifivr,-1 ! ______ loop over vars in desc. order
|
|---|
| 163 |
|
|---|
| 164 | lnb = .false. ! = true, if situation noted above takes place
|
|---|
| 165 |
|
|---|
| 166 | iv=iorvr(io) ! index,
|
|---|
| 167 | it=ityvr(iv) ! type,
|
|---|
| 168 | ia=iatvr(iv) ! primary mov. atom,
|
|---|
| 169 | ib=iowat(ia) ! "base" of current var.
|
|---|
| 170 |
|
|---|
| 171 | xb=xat(ib)
|
|---|
| 172 | yb=yat(ib)
|
|---|
| 173 | zb=zat(ib)
|
|---|
| 174 |
|
|---|
| 175 | ! ---------------------------------------- axis for var.
|
|---|
| 176 |
|
|---|
| 177 | if (it.eq.3) then ! torsion
|
|---|
| 178 |
|
|---|
| 179 | ex= xtoat(ib)
|
|---|
| 180 | ey= ytoat(ib)
|
|---|
| 181 | ez= ztoat(ib)
|
|---|
| 182 |
|
|---|
| 183 | if (ib.eq.ix2) lnb = .true.
|
|---|
| 184 |
|
|---|
| 185 | elseif (it.eq.2) then ! b.angle
|
|---|
| 186 |
|
|---|
| 187 | ex= xbaat(ia)
|
|---|
| 188 | ey= ybaat(ia)
|
|---|
| 189 | ez= zbaat(ia)
|
|---|
| 190 |
|
|---|
| 191 | if (ib.eq.ix2) lnb = .true.
|
|---|
| 192 |
|
|---|
| 193 | elseif (it.eq.1) then ! b.length
|
|---|
| 194 |
|
|---|
| 195 | ex=xtoat(ia)
|
|---|
| 196 | ey=ytoat(ia)
|
|---|
| 197 | ez=ztoat(ia)
|
|---|
| 198 |
|
|---|
| 199 | if (ia.eq.ix2) lnb = .true.
|
|---|
| 200 |
|
|---|
| 201 | endif
|
|---|
| 202 |
|
|---|
| 203 | xfiv=0.0
|
|---|
| 204 | yfiv=0.0
|
|---|
| 205 | zfiv=0.0
|
|---|
| 206 | xfriv=0.0
|
|---|
| 207 | yfriv=0.0
|
|---|
| 208 | zfriv=0.0
|
|---|
| 209 |
|
|---|
| 210 | if (.not.lnb) then
|
|---|
| 211 |
|
|---|
| 212 | i2s=i1s-1 ! last m.s &
|
|---|
| 213 | i1s=imsvr1(iv) ! 1st m.s for var. index 'iv'
|
|---|
| 214 |
|
|---|
| 215 | do ims=i1s,i2s ! __ loop over moving sets
|
|---|
| 216 |
|
|---|
| 217 | i1=latms1(ims) ! 1st &
|
|---|
| 218 | i2=latms2(ims) ! last mov. atom in mov. set 'ims'
|
|---|
| 219 |
|
|---|
| 220 | do i=i1,i2 ! __ loop over atoms i ===================
|
|---|
| 221 |
|
|---|
| 222 | xfiv = xfiv + xfat(i) ! f
|
|---|
| 223 | yfiv = yfiv + yfat(i) !
|
|---|
| 224 | zfiv = zfiv + zfat(i) !
|
|---|
| 225 |
|
|---|
| 226 | xfriv = xfriv + xfrat(i) ! g
|
|---|
| 227 | yfriv = yfriv + yfrat(i) !
|
|---|
| 228 | zfriv = zfriv + zfrat(i) !
|
|---|
| 229 |
|
|---|
| 230 | enddo ! ... atoms i
|
|---|
| 231 | enddo ! ... m.s.
|
|---|
| 232 |
|
|---|
| 233 | i2a=i1a-1 ! last &
|
|---|
| 234 | i1a=iadvr1(iv) ! 1st 'added' var. for 'iv'
|
|---|
| 235 |
|
|---|
| 236 | do iad=i1a,i2a ! loop over add. var.
|
|---|
| 237 |
|
|---|
| 238 | lad=ladvr(iad)
|
|---|
| 239 |
|
|---|
| 240 | xfiv = xfiv + xfvr(lad)
|
|---|
| 241 | yfiv = yfiv + yfvr(lad)
|
|---|
| 242 | zfiv = zfiv + zfvr(lad)
|
|---|
| 243 | xfriv = xfriv + xfrvr(lad)
|
|---|
| 244 | yfriv = yfriv + yfrvr(lad)
|
|---|
| 245 | zfriv = zfriv + zfrvr(lad)
|
|---|
| 246 |
|
|---|
| 247 | enddo
|
|---|
| 248 |
|
|---|
| 249 | else
|
|---|
| 250 |
|
|---|
| 251 | do ivw=ivwat1(ia),ivwat2(ia) ! vdW-domains of 'ia'
|
|---|
| 252 | do j=lvwat1(ivw),lvwat2(ivw) ! .. their atoms
|
|---|
| 253 |
|
|---|
| 254 | xfiv = xfiv - xfat(j)
|
|---|
| 255 | yfiv = yfiv - yfat(j)
|
|---|
| 256 | zfiv = zfiv - zfat(j)
|
|---|
| 257 |
|
|---|
| 258 | xfriv = xfriv - xfrat(j)
|
|---|
| 259 | yfriv = yfriv - yfrat(j)
|
|---|
| 260 | zfriv = zfriv - zfrat(j)
|
|---|
| 261 |
|
|---|
| 262 | enddo
|
|---|
| 263 | enddo
|
|---|
| 264 |
|
|---|
| 265 | do i14=i14at1(ia),i14at2(ia) ! 1-4 partn. of 'ia'
|
|---|
| 266 | j=l14at(i14)
|
|---|
| 267 |
|
|---|
| 268 | xfiv = xfiv - xfat(j)
|
|---|
| 269 | yfiv = yfiv - yfat(j)
|
|---|
| 270 | zfiv = zfiv - zfat(j)
|
|---|
| 271 |
|
|---|
| 272 | xfriv = xfriv - xfrat(j)
|
|---|
| 273 | yfriv = yfriv - yfrat(j)
|
|---|
| 274 | zfriv = zfriv - zfrat(j)
|
|---|
| 275 |
|
|---|
| 276 | enddo
|
|---|
| 277 |
|
|---|
| 278 | endif
|
|---|
| 279 |
|
|---|
| 280 | xfvr(iv) = xfiv
|
|---|
| 281 | yfvr(iv) = yfiv
|
|---|
| 282 | zfvr(iv) = zfiv
|
|---|
| 283 | xfrvr(iv) = xfriv
|
|---|
| 284 | yfrvr(iv) = yfriv
|
|---|
| 285 | zfrvr(iv) = zfriv
|
|---|
| 286 |
|
|---|
| 287 | if (it.eq.3.or.it.eq.2) then ! torsion,b.angle
|
|---|
| 288 |
|
|---|
| 289 | gdeyrg(iv)= (ey*zb-ez*yb)*xfiv+(ez*xb-ex*zb)*yfiv+
|
|---|
| 290 | & (ex*yb-ey*xb)*zfiv
|
|---|
| 291 | & +ex*xfriv+ey*yfriv+ez*zfriv
|
|---|
| 292 |
|
|---|
| 293 | elseif (it.eq.1) then ! b.length
|
|---|
| 294 |
|
|---|
| 295 | gdeyrg(iv)= -(ex*xfiv+ey*yfiv+ez*zfiv)
|
|---|
| 296 |
|
|---|
| 297 | endif
|
|---|
| 298 |
|
|---|
| 299 | if (tesgrd) call gdtreg(nml,iv)
|
|---|
| 300 |
|
|---|
| 301 | enddo ! ... variables in desc. order
|
|---|
| 302 |
|
|---|
| 303 | return
|
|---|
| 304 | end
|
|---|
| 305 | ! **************************
|
|---|
| 306 | subroutine gdtgbl(nml)
|
|---|
| 307 | !
|
|---|
| 308 | ! CALLS: bldmol,enyreg
|
|---|
| 309 | !
|
|---|
| 310 | ! -------------------------- gradtest for 'gbpr'
|
|---|
| 311 |
|
|---|
| 312 | include 'INCL.H'
|
|---|
| 313 |
|
|---|
| 314 | double precision del, pro, gdn, enyreg
|
|---|
| 315 |
|
|---|
| 316 | integer ii, nml, i
|
|---|
| 317 |
|
|---|
| 318 | parameter (del=1.d-7)
|
|---|
| 319 |
|
|---|
| 320 |
|
|---|
| 321 | ii=(nml-1)*6
|
|---|
| 322 |
|
|---|
| 323 | do i = 1,6
|
|---|
| 324 |
|
|---|
| 325 | ! ----------------------------- modify
|
|---|
| 326 | pro = gbpr(i,nml)
|
|---|
| 327 | gbpr(i,nml) = pro+del
|
|---|
| 328 | call bldmol(nml)
|
|---|
| 329 |
|
|---|
| 330 | gdn = ( enyreg(nml) - eyrg ) / del
|
|---|
| 331 |
|
|---|
| 332 | write (logString, *) ' Gb. var #',(ii+i),': ',gdeygb(ii+i),gdn,
|
|---|
| 333 | & abs(gdn-gdeygb(ii+i))
|
|---|
| 334 | ! ----------------------------- restore
|
|---|
| 335 | gbpr(i,nml) = pro
|
|---|
| 336 | call bldmol(nml)
|
|---|
| 337 |
|
|---|
| 338 | enddo ! pars.
|
|---|
| 339 |
|
|---|
| 340 | return
|
|---|
| 341 | end
|
|---|
| 342 | ! *****************************
|
|---|
| 343 | subroutine gdtreg(nml,iv)
|
|---|
| 344 |
|
|---|
| 345 | ! .................................................................
|
|---|
| 346 | ! PURPOSE: calculate partial derivative of reg. energy for molecule
|
|---|
| 347 | ! 'nml' vs. variable 'iv' NUMERICALLY and compare with
|
|---|
| 348 | ! its value obtained analytically
|
|---|
| 349 | !
|
|---|
| 350 | ! CALLS: setvar, enyreg
|
|---|
| 351 | ! .................................................................
|
|---|
| 352 |
|
|---|
| 353 | include 'INCL.H'
|
|---|
| 354 |
|
|---|
| 355 | double precision del, vlvrx, ovr, eynw, enyreg, gdn, gda
|
|---|
| 356 |
|
|---|
| 357 | integer i, it, iv, nml
|
|---|
| 358 |
|
|---|
| 359 | parameter (del=1.d-6)
|
|---|
| 360 |
|
|---|
| 361 | dimension vlvrx(mxvr)
|
|---|
| 362 |
|
|---|
| 363 | ! ____________________________ get & save values of variables
|
|---|
| 364 | do i=1,ivrml1(ntlml)+nvrml(ntlml)-1
|
|---|
| 365 | it=ityvr(i) ! type
|
|---|
| 366 | if (it.eq.3) then ! torsion
|
|---|
| 367 | vlvrx(i)=toat(iatvr(i))
|
|---|
| 368 | elseif (it.eq.2) then ! b.angle
|
|---|
| 369 | vlvrx(i)=baat(iatvr(i))
|
|---|
| 370 | elseif (it.eq.1) then ! b.length
|
|---|
| 371 | vlvrx(i)=blat(iatvr(i))
|
|---|
| 372 | endif
|
|---|
| 373 | enddo
|
|---|
| 374 |
|
|---|
| 375 | ovr=vlvrx(iv)
|
|---|
| 376 | vlvrx(iv)=ovr+del ! change variable 'iv' by 'del'
|
|---|
| 377 | call setvar(nml,vlvrx)
|
|---|
| 378 |
|
|---|
| 379 | eynw=enyreg(nml)
|
|---|
| 380 |
|
|---|
| 381 | gdn=(eynw-eyrg)/del ! numerical derivative
|
|---|
| 382 | gda=gdeyrg(iv) ! analytical der.
|
|---|
| 383 |
|
|---|
| 384 | write (logString, '(1x,2a,2(e12.6,a))') nmvr(iv),': ',gda,' (',
|
|---|
| 385 | & abs(gda-gdn),')'
|
|---|
| 386 |
|
|---|
| 387 | ! _________________________ restore vars
|
|---|
| 388 | vlvrx(iv)=ovr
|
|---|
| 389 | call setvar(nml,vlvrx)
|
|---|
| 390 |
|
|---|
| 391 | return
|
|---|
| 392 | end
|
|---|
| 393 |
|
|---|
