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 10477 : PLUMED_REGISTER_ACTION(RDC,"RDC")
221 10419 : PLUMED_REGISTER_ACTION(RDC,"PCS")
222 :
223 31 : void RDC::registerKeywords( Keywords& keys ) {
224 31 : componentsAreNotOptional(keys);
225 31 : MetainferenceBase::registerKeywords(keys);
226 62 : keys.addFlag("NOPBC",false,"ignore the periodic boundary conditions when calculating distances");
227 62 : keys.add("numbered","ATOMS","the couple of atoms involved in each of the bonds for which you wish to calculate the RDC. "
228 : "Keywords like ATOMS1, ATOMS2, ATOMS3,... should be listed and one dipolar coupling will be "
229 : "calculated for each ATOMS keyword you specify.");
230 62 : keys.reset_style("ATOMS","atoms");
231 62 : keys.add("compulsory","GYROM","1.","Add the product of the gyromagnetic constants for the bond. ");
232 62 : keys.add("compulsory","SCALE","1.","Add the scaling factor to take into account concentration and other effects. ");
233 62 : keys.addFlag("SVD",false,"Set to TRUE if you want to back calculate using Single Value Decomposition (need GSL at compilation time).");
234 62 : keys.add("numbered","COUPLING","Add an experimental value for each coupling (needed by SVD and useful for \\ref STATS).");
235 62 : keys.addOutputComponent("rdc","default","the calculated # RDC");
236 62 : keys.addOutputComponent("exp","SVD/COUPLING","the experimental # RDC");
237 62 : keys.addOutputComponent("Sxx","SVD","Tensor component");
238 62 : keys.addOutputComponent("Syy","SVD","Tensor component");
239 62 : keys.addOutputComponent("Szz","SVD","Tensor component");
240 62 : keys.addOutputComponent("Sxy","SVD","Tensor component");
241 62 : keys.addOutputComponent("Sxz","SVD","Tensor component");
242 62 : keys.addOutputComponent("Syz","SVD","Tensor component");
243 31 : }
244 :
245 29 : RDC::RDC(const ActionOptions&ao):
246 : PLUMED_METAINF_INIT(ao),
247 29 : Const(1.),
248 29 : mu_s(1.),
249 29 : scale(1.),
250 29 : pbc(true)
251 : {
252 29 : bool nopbc=!pbc;
253 29 : parseFlag("NOPBC",nopbc);
254 29 : pbc=!nopbc;
255 :
256 : const double RDCConst = 0.3356806;
257 : const double PCSConst = 1.0;
258 :
259 29 : if( getName().find("RDC")!=std::string::npos) { Const *= RDCConst; }
260 0 : else if( getName().find("PCS")!=std::string::npos) { Const *= PCSConst; }
261 :
262 : // Read in the atoms
263 : std::vector<AtomNumber> t, atoms;
264 29 : for(int i=1;; ++i ) {
265 292 : parseAtomList("ATOMS", i, t );
266 146 : if( t.empty() ) break;
267 117 : if( t.size()!=2 ) {
268 0 : std::string ss; Tools::convert(i,ss);
269 0 : error("ATOMS" + ss + " keyword has the wrong number of atoms");
270 : }
271 117 : atoms.push_back(t[0]);
272 117 : atoms.push_back(t[1]);
273 117 : t.resize(0);
274 117 : }
275 :
276 29 : const unsigned ndata = atoms.size()/2;
277 :
278 : // Read in GYROMAGNETIC constants
279 29 : parse("GYROM", mu_s);
280 29 : if(mu_s==0.) error("GYROM cannot be 0");
281 :
282 : // Read in SCALING factors
283 29 : parse("SCALE", scale);
284 29 : if(scale==0.) error("SCALE cannot be 0");
285 :
286 29 : svd=false;
287 29 : parseFlag("SVD",svd);
288 : #ifndef __PLUMED_HAS_GSL
289 : if(svd) error("You CANNOT use SVD without GSL. Recompile PLUMED with GSL!\n");
290 : #endif
291 29 : if(svd&&getDoScore()) error("It is not possible to use SVD and METAINFERENCE together");
292 :
293 : // Optionally add an experimental value
294 29 : coupl.resize( ndata );
295 : unsigned ntarget=0;
296 82 : for(unsigned i=0; i<ndata; ++i) {
297 138 : if( !parseNumbered( "COUPLING", i+1, coupl[i] ) ) break;
298 53 : ntarget++;
299 : }
300 : bool addexp=false;
301 29 : if(ntarget!=ndata && ntarget!=0) error("found wrong number of COUPLING values");
302 29 : if(ntarget==ndata) addexp=true;
303 29 : if(getDoScore()&&!addexp) error("with DOSCORE you need to set the COUPLING values");
304 29 : if(svd&&!addexp) error("with SVD you need to set the COUPLING values");
305 :
306 :
307 : // Output details of all contacts
308 29 : log.printf(" Gyromagnetic moment is %f. Scaling factor is %f.",mu_s,scale);
309 146 : for(unsigned i=0; i<ndata; ++i) {
310 117 : log.printf(" The %uth Bond Dipolar Coupling is calculated from atoms : %d %d.", i+1, atoms[2*i].serial(), atoms[2*i+1].serial());
311 117 : if(addexp) log.printf(" Experimental coupling is %f.", coupl[i]);
312 117 : log.printf("\n");
313 : }
314 :
315 29 : log<<" Bibliography "
316 58 : <<plumed.cite("Camilloni C, Vendruscolo M, J. Phys. Chem. B 119, 653 (2015)")
317 116 : <<plumed.cite("Camilloni C, Vendruscolo M, Biochemistry 54, 7470 (2015)");
318 87 : log<< plumed.cite("Bonomi, Camilloni, Bioinformatics, 33, 3999 (2017)") << "\n";
319 :
320 :
321 29 : if(!getDoScore()&&!svd) {
322 80 : for(unsigned i=0; i<ndata; i++) {
323 64 : std::string num; Tools::convert(i,num);
324 64 : addComponentWithDerivatives("rdc-"+num);
325 128 : componentIsNotPeriodic("rdc-"+num);
326 : }
327 16 : if(addexp) {
328 0 : for(unsigned i=0; i<ndata; i++) {
329 0 : std::string num; Tools::convert(i,num);
330 0 : addComponent("exp-"+num);
331 0 : componentIsNotPeriodic("exp-"+num);
332 0 : Value* comp=getPntrToComponent("exp-"+num);
333 0 : comp->set(coupl[i]);
334 : }
335 : }
336 : } else {
337 66 : for(unsigned i=0; i<ndata; i++) {
338 53 : std::string num; Tools::convert(i,num);
339 53 : addComponentWithDerivatives("rdc-"+num);
340 106 : componentIsNotPeriodic("rdc-"+num);
341 : }
342 66 : for(unsigned i=0; i<ndata; i++) {
343 53 : std::string num; Tools::convert(i,num);
344 53 : addComponent("exp-"+num);
345 53 : componentIsNotPeriodic("exp-"+num);
346 53 : Value* comp=getPntrToComponent("exp-"+num);
347 53 : comp->set(coupl[i]);
348 : }
349 : }
350 :
351 29 : if(svd) {
352 2 : addComponent("Sxx"); componentIsNotPeriodic("Sxx");
353 2 : addComponent("Syy"); componentIsNotPeriodic("Syy");
354 2 : addComponent("Szz"); componentIsNotPeriodic("Szz");
355 2 : addComponent("Sxy"); componentIsNotPeriodic("Sxy");
356 2 : addComponent("Sxz"); componentIsNotPeriodic("Sxz");
357 3 : addComponent("Syz"); componentIsNotPeriodic("Syz");
358 : }
359 :
360 29 : requestAtoms(atoms, false);
361 29 : if(getDoScore()) {
362 12 : setParameters(coupl);
363 12 : Initialise(coupl.size());
364 : }
365 29 : setDerivatives();
366 29 : checkRead();
367 29 : }
368 :
369 5 : void RDC::do_svd()
370 : {
371 : #ifdef __PLUMED_HAS_GSL
372 5 : gsl_vector_unique_ptr rdc_vec(gsl_vector_alloc(coupl.size())),
373 5 : S(gsl_vector_alloc(5)),
374 5 : Stmp(gsl_vector_alloc(5)),
375 5 : work(gsl_vector_alloc(5)),
376 5 : bc(gsl_vector_alloc(coupl.size()));
377 :
378 5 : gsl_matrix_unique_ptr coef_mat(gsl_matrix_alloc(coupl.size(),5)),
379 5 : A(gsl_matrix_alloc(coupl.size(),5)),
380 5 : V(gsl_matrix_alloc(5,5));
381 :
382 5 : gsl_matrix_set_zero(coef_mat.get());
383 5 : gsl_vector_set_zero(bc.get());
384 :
385 : unsigned index=0;
386 5 : std::vector<double> dmax(coupl.size());
387 30 : for(unsigned r=0; r<getNumberOfAtoms(); r+=2) {
388 25 : Vector distance;
389 25 : if(pbc) distance = pbcDistance(getPosition(r),getPosition(r+1));
390 0 : else distance = delta(getPosition(r),getPosition(r+1));
391 25 : double d = distance.modulo();
392 25 : double d2 = d*d;
393 25 : double d3 = d2*d;
394 25 : double id3 = 1./d3;
395 25 : double max = -Const*mu_s*scale;
396 25 : dmax[index] = id3*max;
397 25 : double mu_x = distance[0]/d;
398 25 : double mu_y = distance[1]/d;
399 25 : double mu_z = distance[2]/d;
400 25 : gsl_vector_set(rdc_vec.get(),index,coupl[index]/dmax[index]);
401 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));
402 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));
403 25 : gsl_matrix_set(coef_mat.get(),index,2,gsl_matrix_get(coef_mat.get(),index,2)+(2.0*mu_x*mu_y));
404 25 : gsl_matrix_set(coef_mat.get(),index,3,gsl_matrix_get(coef_mat.get(),index,3)+(2.0*mu_x*mu_z));
405 25 : gsl_matrix_set(coef_mat.get(),index,4,gsl_matrix_get(coef_mat.get(),index,4)+(2.0*mu_y*mu_z));
406 25 : index++;
407 : }
408 5 : gsl_matrix_memcpy(A.get(),coef_mat.get());
409 5 : gsl_linalg_SV_decomp(A.get(), V.get(), Stmp.get(), work.get());
410 5 : gsl_linalg_SV_solve(A.get(), V.get(), Stmp.get(), rdc_vec.get(), S.get());
411 : /* tensor */
412 : Value* tensor;
413 5 : tensor=getPntrToComponent("Sxx");
414 5 : double Sxx = gsl_vector_get(S.get(),0);
415 : tensor->set(Sxx);
416 5 : tensor=getPntrToComponent("Syy");
417 5 : double Syy = gsl_vector_get(S.get(),1);
418 : tensor->set(Syy);
419 5 : tensor=getPntrToComponent("Szz");
420 5 : double Szz = -Sxx-Syy;
421 : tensor->set(Szz);
422 5 : tensor=getPntrToComponent("Sxy");
423 5 : double Sxy = gsl_vector_get(S.get(),2);
424 : tensor->set(Sxy);
425 5 : tensor=getPntrToComponent("Sxz");
426 5 : double Sxz = gsl_vector_get(S.get(),3);
427 : tensor->set(Sxz);
428 5 : tensor=getPntrToComponent("Syz");
429 5 : double Syz = gsl_vector_get(S.get(),4);
430 : tensor->set(Syz);
431 :
432 5 : gsl_blas_dgemv(CblasNoTrans, 1.0, coef_mat.get(), S.get(), 0., bc.get());
433 30 : for(index=0; index<coupl.size(); index++) {
434 25 : double rdc = gsl_vector_get(bc.get(),index)*dmax[index];
435 25 : Value* val=getPntrToComponent(index);
436 : val->set(rdc);
437 : }
438 : #endif
439 5 : }
440 :
441 2172 : void RDC::calculate()
442 : {
443 2172 : if(svd) {
444 5 : do_svd();
445 5 : return;
446 : }
447 :
448 2167 : const double max = -Const*scale*mu_s;
449 : const unsigned N=getNumberOfAtoms();
450 2167 : std::vector<Vector> dRDC(N/2, Vector{0.,0.,0.});
451 :
452 : /* RDC Calculations and forces */
453 2167 : #pragma omp parallel num_threads(OpenMP::getNumThreads())
454 : {
455 : #pragma omp for
456 : for(unsigned r=0; r<N; r+=2)
457 : {
458 : const unsigned index=r/2;
459 : Vector distance;
460 : if(pbc) distance = pbcDistance(getPosition(r),getPosition(r+1));
461 : else distance = delta(getPosition(r),getPosition(r+1));
462 : const double d2 = distance.modulo2();
463 : const double ind = 1./std::sqrt(d2);
464 : const double ind2 = 1./d2;
465 : const double ind3 = ind2*ind;
466 : const double x2 = distance[0]*distance[0]*ind2;
467 : const double y2 = distance[1]*distance[1]*ind2;
468 : const double z2 = distance[2]*distance[2]*ind2;
469 : const double dmax = ind3*max;
470 : const double ddmax = dmax*ind2;
471 :
472 : const double rdc = 0.5*dmax*(3.*z2-1.);
473 : const double prod_xy = (x2+y2-4.*z2);
474 : const double prod_z = (3.*x2 + 3.*y2 - 2.*z2);
475 :
476 : dRDC[index] = -1.5*ddmax*distance;
477 : dRDC[index][0] *= prod_xy;
478 : dRDC[index][1] *= prod_xy;
479 : dRDC[index][2] *= prod_z;
480 :
481 : std::string num; Tools::convert(index,num);
482 : Value* val=getPntrToComponent("rdc-"+num);
483 : val->set(rdc);
484 : if(!getDoScore()) {
485 : setBoxDerivatives(val, Tensor(distance,dRDC[index]));
486 : setAtomsDerivatives(val, r, dRDC[index]);
487 : setAtomsDerivatives(val, r+1, -dRDC[index]);
488 : } else setCalcData(index, rdc);
489 : }
490 : }
491 :
492 2167 : if(getDoScore()) {
493 : /* Metainference */
494 1824 : Tensor dervir;
495 1824 : double score = getScore();
496 : setScore(score);
497 :
498 : /* calculate final derivatives */
499 1824 : Value* val=getPntrToComponent("score");
500 9120 : for(unsigned r=0; r<N; r+=2)
501 : {
502 7296 : const unsigned index=r/2;
503 7296 : Vector distance;
504 7296 : if(pbc) distance = pbcDistance(getPosition(r),getPosition(r+1));
505 0 : else distance = delta(getPosition(r),getPosition(r+1));
506 7296 : const Vector der = dRDC[index]*getMetaDer(index);
507 7296 : dervir += Tensor(distance, der);
508 7296 : setAtomsDerivatives(val, r, der);
509 7296 : setAtomsDerivatives(val, r+1, -der);
510 : }
511 1824 : setBoxDerivatives(val, dervir);
512 : }
513 : }
514 :
515 327 : void RDC::update() {
516 : // write status file
517 327 : if(getWstride()>0&& (getStep()%getWstride()==0 || getCPT()) ) writeStatus();
518 327 : }
519 :
520 : }
521 : }
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