Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2014-2023 The plumed team
3 : (see the PEOPLE file at the root of the distribution for a list of names)
4 :
5 : See http://www.plumed.org for more information.
6 :
7 : This file is part of plumed, version 2.
8 :
9 : plumed is free software: you can redistribute it and/or modify
10 : it under the terms of the GNU Lesser General Public License as published by
11 : the Free Software Foundation, either version 3 of the License, or
12 : (at your option) any later version.
13 :
14 : plumed is distributed in the hope that it will be useful,
15 : but WITHOUT ANY WARRANTY; without even the implied warranty of
16 : MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17 : GNU Lesser General Public License for more details.
18 :
19 : You should have received a copy of the GNU Lesser General Public License
20 : along with plumed. If not, see <http://www.gnu.org/licenses/>.
21 : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
22 : #include "MetainferenceBase.h"
23 : #include "core/ActionRegister.h"
24 : #include "tools/Pbc.h"
25 :
26 : #ifdef __PLUMED_HAS_GSL
27 : #include <gsl/gsl_vector.h>
28 : #include <gsl/gsl_matrix.h>
29 : #include <gsl/gsl_linalg.h>
30 : #include <gsl/gsl_blas.h>
31 : #endif
32 :
33 : namespace PLMD {
34 : namespace isdb {
35 :
36 : //+PLUMEDOC ISDB_COLVAR RDC
37 : /*
38 : Calculates the (Residual) Dipolar Coupling between two atoms.
39 :
40 : The Dipolar Coupling between two nuclei depends on the \f$\theta\f$ angle between
41 : the inter-nuclear vector and the external magnetic field.
42 :
43 : \f[
44 : D=D_{max}0.5(3\cos^2(\theta)-1)
45 : \f]
46 :
47 : where
48 :
49 : \f[
50 : D_{max}=-\mu_0\gamma_1\gamma_2h/(8\pi^3r^3)
51 : \f]
52 :
53 : that is the maximal value of the dipolar coupling for the two nuclear spins with gyromagnetic ratio \f$\gamma\f$.
54 : \f$\mu\f$ is the magnetic constant and h is the Planck constant.
55 :
56 : Common Gyromagnetic Ratios (C.G.S)
57 : - H(1) 26.7513
58 : - C(13) 6.7261
59 : - N(15) -2.7116
60 : and their products (this is what is given in input using the keyword GYROM)
61 : - N-H -72.5388
62 : - C-H 179.9319
63 : - C-N -18.2385
64 : - C-C 45.2404
65 :
66 : In isotropic media DCs average to zero because of the rotational
67 : averaging, but when the rotational symmetry is broken, either through the introduction of an alignment medium or for molecules
68 : with highly anisotropic paramagnetic susceptibility, then the average of the DCs is not zero and it is possible to measure a Residual Dipolar Coupling (RDCs).
69 :
70 : This collective variable calculates the Dipolar Coupling for a set of couple of atoms using
71 : the above definition.
72 :
73 : In a standard MD simulation the average over time of the DC should then be zero. If one wants to model the meaning of a set of measured RDCs it is possible to try to solve the following problem: "what is the distribution of structures and orientations that reproduce the measured RDCs".
74 :
75 : This collective variable can then be use to break the rotational symmetry of a simulation by imposing that the average of the DCs over the conformational ensemble must be equal to the measured RDCs \cite Camilloni:2015ka . Since measured RDCs are also a function of the fraction of aligned molecules in the sample it is better to compare them modulo a constant or looking at the correlation.
76 :
77 : Alternatively if the molecule is rigid it is possible to use the experimental data to calculate the alignment tensor and the use that to back calculate the RDCs, this is what is usually call the Single Value Decomposition approach. In this case the code rely on the
78 : a set of function from the GNU Scientific Library (GSL). (With SVD forces are not currently implemented).
79 :
80 : Replica-Averaged simulations can be performed using RDCs, \ref ENSEMBLE, \ref STATS and \ref RESTRAINT .
81 : \ref METAINFERENCE can be activated using DOSCORE and the other relevant keywords.
82 :
83 : Additional material and examples can be also found in the tutorial \ref isdb-1
84 :
85 : \par Examples
86 : In the following example five N-H RDCs are defined and averaged over multiple replicas,
87 : their correlation is then calculated with respect to a set of experimental data and restrained.
88 : In addition, and only for analysis purposes, the same RDCs each single conformation are calculated
89 : using a Single Value Decomposition algorithm, then averaged and again compared with the experimental data.
90 :
91 : \plumedfile
92 : #SETTINGS NREPLICAS=2
93 : RDC ...
94 : GYROM=-72.5388
95 : SCALE=0.001
96 : ATOMS1=20,21
97 : ATOMS2=37,38
98 : ATOMS3=56,57
99 : ATOMS4=76,77
100 : ATOMS5=92,93
101 : LABEL=nh
102 : ... RDC
103 :
104 : erdc: ENSEMBLE ARG=nh.*
105 :
106 : st: STATS ARG=erdc.* PARAMETERS=8.17,-8.271,-10.489,-9.871,-9.152
107 :
108 : rdce: RESTRAINT ARG=st.corr KAPPA=0. SLOPE=-25000.0 AT=1.
109 :
110 : RDC ...
111 : GYROM=-72.5388
112 : SVD
113 : ATOMS1=20,21 COUPLING1=8.17
114 : ATOMS2=37,38 COUPLING2=-8.271
115 : ATOMS3=56,57 COUPLING3=-10.489
116 : ATOMS4=76,77 COUPLING4=-9.871
117 : ATOMS5=92,93 COUPLING5=-9.152
118 : LABEL=svd
119 : ... RDC
120 :
121 : esvd: ENSEMBLE ARG=(svd\.rdc-.*)
122 :
123 : st_svd: STATS ARG=esvd.* PARAMETERS=8.17,-8.271,-10.489,-9.871,-9.152
124 :
125 : PRINT ARG=st.corr,st_svd.corr,rdce.bias FILE=colvar
126 : \endplumedfile
127 :
128 : */
129 : //+ENDPLUMEDOC
130 :
131 : //+PLUMEDOC ISDB_COLVAR PCS
132 : /*
133 : Calculates the Pseudo-contact shift of a nucleus determined by the presence of a metal ion susceptible to anisotropic magnetization.
134 :
135 : The PCS of an atomic nucleus depends on the \f$\theta\f$ angle between the vector from the spin-label to the nucleus
136 : and the external magnetic field and the module of the vector itself \cite Camilloni:2015jf . While in principle the averaging
137 : resulting from the tumbling should remove the pseudo-contact shift, in presence of the NMR magnetic field the magnetically anisotropic molecule bound to system will break the rotational symmetry does resulting in measurable values for the PCS and RDC.
138 :
139 : PCS values can also be calculated using a Single Value Decomposition approach, in this case the code rely on the
140 : a set of function from the GNU Scientific Library (GSL). (With SVD forces are not currently implemented).
141 :
142 : Replica-Averaged simulations can be performed using PCS values, \ref ENSEMBLE, \ref STATS and \ref RESTRAINT .
143 : Metainference simulations can be performed with this CV and \ref METAINFERENCE .
144 :
145 : \par Examples
146 :
147 : In the following example five PCS values are defined and their correlation with
148 : respect to a set of experimental data is calculated and restrained. In addition,
149 : and only for analysis purposes, the same PCS values are calculated using a Single Value
150 : Decomposition algorithm.
151 :
152 : \plumedfile
153 : PCS ...
154 : ATOMS1=20,21
155 : ATOMS2=20,38
156 : ATOMS3=20,57
157 : ATOMS4=20,77
158 : ATOMS5=20,93
159 : LABEL=nh
160 : ... PCS
161 :
162 : enh: ENSEMBLE ARG=nh.*
163 :
164 : st: STATS ARG=enh.* PARAMETERS=8.17,-8.271,-10.489,-9.871,-9.152
165 :
166 : pcse: RESTRAINT ARG=st.corr KAPPA=0. SLOPE=-25000.0 AT=1.
167 :
168 : PRINT ARG=st.corr,pcse.bias FILE=colvar
169 : \endplumedfile
170 :
171 : */
172 : //+ENDPLUMEDOC
173 :
174 : class RDC :
175 : public MetainferenceBase
176 : {
177 : private:
178 : double Const;
179 : double mu_s;
180 : double scale;
181 : std::vector<double> coupl;
182 : bool svd;
183 : bool pbc;
184 :
185 : #ifdef __PLUMED_HAS_GSL
186 : /// Auxiliary class to delete a gsl_vector.
187 : /// If used somewhere else we can move it.
188 : struct gsl_vector_deleter {
189 : void operator()(gsl_vector* p) {
190 25 : gsl_vector_free(p);
191 25 : }
192 : };
193 :
194 : /// unique_ptr to a gsl_vector.
195 : /// Gets deleted when going out of scope.
196 : typedef std::unique_ptr<gsl_vector,gsl_vector_deleter> gsl_vector_unique_ptr;
197 :
198 : /// Auxiliary class to delete a gsl_matrix.
199 : /// If used somewhere else we can move it.
200 : struct gsl_matrix_deleter {
201 : void operator()(gsl_matrix* p) {
202 15 : gsl_matrix_free(p);
203 15 : }
204 : };
205 :
206 : /// unique_ptr to a gsl_matrix.
207 : /// Gets deleted when going out of scope.
208 : typedef std::unique_ptr<gsl_matrix,gsl_matrix_deleter> gsl_matrix_unique_ptr;
209 : #endif
210 :
211 :
212 : void do_svd();
213 : public:
214 : explicit RDC(const ActionOptions&);
215 : static void registerKeywords( Keywords& keys );
216 : void calculate() override;
217 : void update() override;
218 : };
219 :
220 : PLUMED_REGISTER_ACTION(RDC,"RDC")
221 : PLUMED_REGISTER_ACTION(RDC,"PCS")
222 :
223 33 : void RDC::registerKeywords( Keywords& keys ) {
224 33 : MetainferenceBase::registerKeywords(keys);
225 66 : keys.addFlag("NOPBC",false,"ignore the periodic boundary conditions when calculating distances");
226 66 : keys.add("numbered","ATOMS","the couple of atoms involved in each of the bonds for which you wish to calculate the RDC. "
227 : "Keywords like ATOMS1, ATOMS2, ATOMS3,... should be listed and one dipolar coupling will be "
228 : "calculated for each ATOMS keyword you specify.");
229 66 : keys.reset_style("ATOMS","atoms");
230 66 : keys.add("compulsory","GYROM","1.","Add the product of the gyromagnetic constants for the bond. ");
231 66 : keys.add("compulsory","SCALE","1.","Add the scaling factor to take into account concentration and other effects. ");
232 66 : keys.addFlag("SVD",false,"Set to TRUE if you want to back calculate using Single Value Decomposition (need GSL at compilation time).");
233 66 : keys.add("numbered","COUPLING","Add an experimental value for each coupling (needed by SVD and useful for STATS).");
234 66 : keys.addOutputComponent("rdc","default","the calculated # RDC");
235 66 : keys.addOutputComponent("exp","SVD/COUPLING","the experimental # RDC");
236 66 : keys.addOutputComponent("Sxx","SVD","Tensor component");
237 66 : keys.addOutputComponent("Syy","SVD","Tensor component");
238 66 : keys.addOutputComponent("Szz","SVD","Tensor component");
239 66 : keys.addOutputComponent("Sxy","SVD","Tensor component");
240 66 : keys.addOutputComponent("Sxz","SVD","Tensor component");
241 66 : keys.addOutputComponent("Syz","SVD","Tensor component");
242 33 : }
243 :
244 29 : RDC::RDC(const ActionOptions&ao):
245 : PLUMED_METAINF_INIT(ao),
246 29 : Const(1.),
247 29 : mu_s(1.),
248 29 : scale(1.),
249 29 : pbc(true)
250 : {
251 29 : bool nopbc=!pbc;
252 29 : parseFlag("NOPBC",nopbc);
253 29 : pbc=!nopbc;
254 :
255 : const double RDCConst = 0.3356806;
256 : const double PCSConst = 1.0;
257 :
258 29 : if( getName().find("RDC")!=std::string::npos) { Const *= RDCConst; }
259 0 : else if( getName().find("PCS")!=std::string::npos) { Const *= PCSConst; }
260 :
261 : // Read in the atoms
262 : std::vector<AtomNumber> t, atoms;
263 29 : for(int i=1;; ++i ) {
264 292 : parseAtomList("ATOMS", i, t );
265 146 : if( t.empty() ) break;
266 117 : if( t.size()!=2 ) {
267 0 : std::string ss; Tools::convert(i,ss);
268 0 : error("ATOMS" + ss + " keyword has the wrong number of atoms");
269 : }
270 117 : atoms.push_back(t[0]);
271 117 : atoms.push_back(t[1]);
272 117 : t.resize(0);
273 117 : }
274 :
275 29 : const unsigned ndata = atoms.size()/2;
276 :
277 : // Read in GYROMAGNETIC constants
278 29 : parse("GYROM", mu_s);
279 29 : if(mu_s==0.) error("GYROM cannot be 0");
280 :
281 : // Read in SCALING factors
282 29 : parse("SCALE", scale);
283 29 : if(scale==0.) error("SCALE cannot be 0");
284 :
285 29 : svd=false;
286 29 : parseFlag("SVD",svd);
287 : #ifndef __PLUMED_HAS_GSL
288 : if(svd) error("You CANNOT use SVD without GSL. Recompile PLUMED with GSL!\n");
289 : #endif
290 29 : if(svd&&getDoScore()) error("It is not possible to use SVD and METAINFERENCE together");
291 :
292 : // Optionally add an experimental value
293 29 : coupl.resize( ndata );
294 : unsigned ntarget=0;
295 82 : for(unsigned i=0; i<ndata; ++i) {
296 138 : if( !parseNumbered( "COUPLING", i+1, coupl[i] ) ) break;
297 53 : ntarget++;
298 : }
299 : bool addexp=false;
300 29 : if(ntarget!=ndata && ntarget!=0) error("found wrong number of COUPLING values");
301 29 : if(ntarget==ndata) addexp=true;
302 29 : if(getDoScore()&&!addexp) error("with DOSCORE you need to set the COUPLING values");
303 29 : if(svd&&!addexp) error("with SVD you need to set the COUPLING values");
304 :
305 :
306 : // Output details of all contacts
307 29 : log.printf(" Gyromagnetic moment is %f. Scaling factor is %f.",mu_s,scale);
308 146 : for(unsigned i=0; i<ndata; ++i) {
309 117 : log.printf(" The %uth Bond Dipolar Coupling is calculated from atoms : %d %d.", i+1, atoms[2*i].serial(), atoms[2*i+1].serial());
310 117 : if(addexp) log.printf(" Experimental coupling is %f.", coupl[i]);
311 117 : log.printf("\n");
312 : }
313 :
314 29 : log<<" Bibliography "
315 58 : <<plumed.cite("Camilloni C, Vendruscolo M, J. Phys. Chem. B 119, 653 (2015)")
316 87 : <<plumed.cite("Camilloni C, Vendruscolo M, Biochemistry 54, 7470 (2015)");
317 58 : log<< plumed.cite("Bonomi, Camilloni, Bioinformatics, 33, 3999 (2017)") << "\n";
318 :
319 :
320 29 : if(!getDoScore()&&!svd) {
321 80 : for(unsigned i=0; i<ndata; i++) {
322 64 : std::string num; Tools::convert(i,num);
323 128 : addComponentWithDerivatives("rdc-"+num);
324 128 : componentIsNotPeriodic("rdc-"+num);
325 : }
326 16 : if(addexp) {
327 0 : for(unsigned i=0; i<ndata; i++) {
328 0 : std::string num; Tools::convert(i,num);
329 0 : addComponent("exp-"+num);
330 0 : componentIsNotPeriodic("exp-"+num);
331 0 : Value* comp=getPntrToComponent("exp-"+num);
332 0 : comp->set(coupl[i]);
333 : }
334 : }
335 : } else {
336 66 : for(unsigned i=0; i<ndata; i++) {
337 53 : std::string num; Tools::convert(i,num);
338 106 : addComponentWithDerivatives("rdc-"+num);
339 106 : componentIsNotPeriodic("rdc-"+num);
340 : }
341 66 : for(unsigned i=0; i<ndata; i++) {
342 53 : std::string num; Tools::convert(i,num);
343 106 : addComponent("exp-"+num);
344 53 : componentIsNotPeriodic("exp-"+num);
345 53 : Value* comp=getPntrToComponent("exp-"+num);
346 53 : comp->set(coupl[i]);
347 : }
348 : }
349 :
350 29 : if(svd) {
351 3 : addComponent("Sxx"); componentIsNotPeriodic("Sxx");
352 3 : addComponent("Syy"); componentIsNotPeriodic("Syy");
353 3 : addComponent("Szz"); componentIsNotPeriodic("Szz");
354 3 : addComponent("Sxy"); componentIsNotPeriodic("Sxy");
355 3 : addComponent("Sxz"); componentIsNotPeriodic("Sxz");
356 3 : addComponent("Syz"); componentIsNotPeriodic("Syz");
357 : }
358 :
359 29 : requestAtoms(atoms, false);
360 29 : if(getDoScore()) {
361 12 : setParameters(coupl);
362 12 : Initialise(coupl.size());
363 : }
364 29 : setDerivatives();
365 29 : checkRead();
366 29 : }
367 :
368 5 : void RDC::do_svd()
369 : {
370 : #ifdef __PLUMED_HAS_GSL
371 5 : gsl_vector_unique_ptr rdc_vec(gsl_vector_alloc(coupl.size())),
372 5 : S(gsl_vector_alloc(5)),
373 5 : Stmp(gsl_vector_alloc(5)),
374 5 : work(gsl_vector_alloc(5)),
375 5 : bc(gsl_vector_alloc(coupl.size()));
376 :
377 5 : gsl_matrix_unique_ptr coef_mat(gsl_matrix_alloc(coupl.size(),5)),
378 5 : A(gsl_matrix_alloc(coupl.size(),5)),
379 5 : V(gsl_matrix_alloc(5,5));
380 :
381 5 : gsl_matrix_set_zero(coef_mat.get());
382 5 : gsl_vector_set_zero(bc.get());
383 :
384 : unsigned index=0;
385 5 : std::vector<double> dmax(coupl.size());
386 30 : for(unsigned r=0; r<getNumberOfAtoms(); r+=2) {
387 25 : Vector distance;
388 25 : if(pbc) distance = pbcDistance(getPosition(r),getPosition(r+1));
389 0 : else distance = delta(getPosition(r),getPosition(r+1));
390 25 : double d = distance.modulo();
391 25 : double d2 = d*d;
392 25 : double d3 = d2*d;
393 25 : double id3 = 1./d3;
394 25 : double max = -Const*mu_s*scale;
395 25 : dmax[index] = id3*max;
396 25 : double mu_x = distance[0]/d;
397 25 : double mu_y = distance[1]/d;
398 25 : double mu_z = distance[2]/d;
399 25 : gsl_vector_set(rdc_vec.get(),index,coupl[index]/dmax[index]);
400 25 : gsl_matrix_set(coef_mat.get(),index,0,gsl_matrix_get(coef_mat.get(),index,0)+(mu_x*mu_x-mu_z*mu_z));
401 25 : gsl_matrix_set(coef_mat.get(),index,1,gsl_matrix_get(coef_mat.get(),index,1)+(mu_y*mu_y-mu_z*mu_z));
402 25 : gsl_matrix_set(coef_mat.get(),index,2,gsl_matrix_get(coef_mat.get(),index,2)+(2.0*mu_x*mu_y));
403 25 : gsl_matrix_set(coef_mat.get(),index,3,gsl_matrix_get(coef_mat.get(),index,3)+(2.0*mu_x*mu_z));
404 25 : gsl_matrix_set(coef_mat.get(),index,4,gsl_matrix_get(coef_mat.get(),index,4)+(2.0*mu_y*mu_z));
405 25 : index++;
406 : }
407 5 : gsl_matrix_memcpy(A.get(),coef_mat.get());
408 5 : gsl_linalg_SV_decomp(A.get(), V.get(), Stmp.get(), work.get());
409 5 : gsl_linalg_SV_solve(A.get(), V.get(), Stmp.get(), rdc_vec.get(), S.get());
410 : /* tensor */
411 : Value* tensor;
412 5 : tensor=getPntrToComponent("Sxx");
413 5 : double Sxx = gsl_vector_get(S.get(),0);
414 : tensor->set(Sxx);
415 5 : tensor=getPntrToComponent("Syy");
416 5 : double Syy = gsl_vector_get(S.get(),1);
417 : tensor->set(Syy);
418 5 : tensor=getPntrToComponent("Szz");
419 5 : double Szz = -Sxx-Syy;
420 : tensor->set(Szz);
421 5 : tensor=getPntrToComponent("Sxy");
422 5 : double Sxy = gsl_vector_get(S.get(),2);
423 : tensor->set(Sxy);
424 5 : tensor=getPntrToComponent("Sxz");
425 5 : double Sxz = gsl_vector_get(S.get(),3);
426 : tensor->set(Sxz);
427 5 : tensor=getPntrToComponent("Syz");
428 5 : double Syz = gsl_vector_get(S.get(),4);
429 : tensor->set(Syz);
430 :
431 5 : gsl_blas_dgemv(CblasNoTrans, 1.0, coef_mat.get(), S.get(), 0., bc.get());
432 30 : for(index=0; index<coupl.size(); index++) {
433 25 : double rdc = gsl_vector_get(bc.get(),index)*dmax[index];
434 25 : Value* val=getPntrToComponent(index);
435 : val->set(rdc);
436 : }
437 : #endif
438 5 : }
439 :
440 2172 : void RDC::calculate()
441 : {
442 2172 : if(svd) {
443 5 : do_svd();
444 5 : return;
445 : }
446 :
447 2167 : const double max = -Const*scale*mu_s;
448 : const unsigned N=getNumberOfAtoms();
449 2167 : std::vector<Vector> dRDC(N/2, Vector{0.,0.,0.});
450 :
451 : /* RDC Calculations and forces */
452 2167 : #pragma omp parallel num_threads(OpenMP::getNumThreads())
453 : {
454 : #pragma omp for
455 : for(unsigned r=0; r<N; r+=2)
456 : {
457 : const unsigned index=r/2;
458 : Vector distance;
459 : if(pbc) distance = pbcDistance(getPosition(r),getPosition(r+1));
460 : else distance = delta(getPosition(r),getPosition(r+1));
461 : const double d2 = distance.modulo2();
462 : const double ind = 1./std::sqrt(d2);
463 : const double ind2 = 1./d2;
464 : const double ind3 = ind2*ind;
465 : const double x2 = distance[0]*distance[0]*ind2;
466 : const double y2 = distance[1]*distance[1]*ind2;
467 : const double z2 = distance[2]*distance[2]*ind2;
468 : const double dmax = ind3*max;
469 : const double ddmax = dmax*ind2;
470 :
471 : const double rdc = 0.5*dmax*(3.*z2-1.);
472 : const double prod_xy = (x2+y2-4.*z2);
473 : const double prod_z = (3.*x2 + 3.*y2 - 2.*z2);
474 :
475 : dRDC[index] = -1.5*ddmax*distance;
476 : dRDC[index][0] *= prod_xy;
477 : dRDC[index][1] *= prod_xy;
478 : dRDC[index][2] *= prod_z;
479 :
480 : std::string num; Tools::convert(index,num);
481 : Value* val=getPntrToComponent("rdc-"+num);
482 : val->set(rdc);
483 : if(!getDoScore()) {
484 : setBoxDerivatives(val, Tensor(distance,dRDC[index]));
485 : setAtomsDerivatives(val, r, dRDC[index]);
486 : setAtomsDerivatives(val, r+1, -dRDC[index]);
487 : } else setCalcData(index, rdc);
488 : }
489 : }
490 :
491 2167 : if(getDoScore()) {
492 : /* Metainference */
493 1824 : Tensor dervir;
494 1824 : double score = getScore();
495 1824 : setScore(score);
496 :
497 : /* calculate final derivatives */
498 1824 : Value* val=getPntrToComponent("score");
499 9120 : for(unsigned r=0; r<N; r+=2)
500 : {
501 7296 : const unsigned index=r/2;
502 7296 : Vector distance;
503 7296 : if(pbc) distance = pbcDistance(getPosition(r),getPosition(r+1));
504 0 : else distance = delta(getPosition(r),getPosition(r+1));
505 7296 : const Vector der = dRDC[index]*getMetaDer(index);
506 7296 : dervir += Tensor(distance, der);
507 7296 : setAtomsDerivatives(val, r, der);
508 7296 : setAtomsDerivatives(val, r+1, -der);
509 : }
510 1824 : setBoxDerivatives(val, dervir);
511 : }
512 : }
513 :
514 327 : void RDC::update() {
515 : // write status file
516 327 : if(getWstride()>0&& (getStep()%getWstride()==0 || getCPT()) ) writeStatus();
517 327 : }
518 :
519 : }
520 : }
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