Line data Source code
1 : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
2 : Copyright (c) 2011-2023 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 "core/ActionAtomistic.h"
23 : #include "core/ActionPilot.h"
24 : #include "core/ActionRegister.h"
25 : #include "tools/Vector.h"
26 : #include "tools/AtomNumber.h"
27 : #include "tools/Tools.h"
28 : #include "core/PlumedMain.h"
29 : #include "core/ActionSet.h"
30 : #include "core/GenericMolInfo.h"
31 : #include "tools/OpenMP.h"
32 : #include "tools/Tree.h"
33 :
34 : #include <vector>
35 : #include <string>
36 :
37 : namespace PLMD {
38 : namespace generic {
39 :
40 : //+PLUMEDOC GENERIC WHOLEMOLECULES
41 : /*
42 : This action is used to rebuild molecules that can become split by the periodic boundary conditions.
43 :
44 : This command performs an operation that is similar what was done by the ALIGN_ATOMS keyword from plumed1.
45 : This operation is needed as some MD dynamics code (e.g. GROMACS) can break molecules during the calculation.
46 : Whenever we are able we try to ensure that molecules are reconstructed automatically. You thus do not need
47 : to use this action when you are using actions such as [COM](COM.md), [CENTER](CENTER.md), [GYRATION](GYRATION.md)
48 : and so on as the reconstruction of molecules is done automatically in these actions. It is, however, important to understand
49 : molecule reconstruction as there are many cases (e.g. when you are calculating the end-to-end distance of a polymer)
50 : where not using the WHOLEMOLCULES command can cause the artifacts discussed in the attached reference.
51 :
52 : If you think that you need to use this command a good idea is to use the [DUMPATOMS](DUMPATOMS.md) directive
53 : to output the atomic positions. This will allow you to see the effect that including/not including WHOLEMOLECULES
54 : has on the calculation.
55 :
56 : > [!ATTENTION]
57 : > This directive modifies the stored position at the precise moment
58 : > it is executed. This means that only collective variables
59 : > which are below it in the input script will see the corrected positions.
60 : > As a general rule, put it at the top of the input file. Also, unless you
61 : > know exactly what you are doing, leave the default stride (1), so that
62 : > this action is performed at every MD step.
63 :
64 : Notice that the behavior of WHOLEMOLECULES is affected by the last [MOLINFO](MOLINFO.md) action
65 : that is present in the input file before the WHOLEMOLECULES command. Specifically, if the
66 : [MOLINFO](MOLINFO.md) action does not have a `WHOLE` flag, then the behavior is the following:
67 :
68 : - The first atom of the list is left in place
69 : - Each atom of the list is shifted by a lattice vectors so that it becomes as close as possible
70 : to the previous one, iteratively.
71 :
72 : In this way, if an entity consists of a list of atoms such that consecutive atoms in the
73 : list are always closer than half a box side the entity will become whole.
74 : This can be usually achieved selecting consecutive atoms (1-100), but it is also possible
75 : to skip some atoms, provided consecutive chosen atoms are close enough.
76 :
77 : If, by contrast, the [MOLINFO](MOLINFO.md) action does have a `WHOLE` flag, then a minimum spanning tree
78 : is built based on the atoms passed to WHOLEMOLECULES using the coordinates in the PDB
79 : passed to [MOLINFO](MOLINFO.md) as a reference, and this tree is used to reconstruct PBCs.
80 : This approach is more robust when dealing with complexes of multiple molecules.
81 :
82 : ## Examples
83 :
84 : This command instructs plumed to reconstruct the molecule containing atoms 1-20
85 : at every step of the calculation and dump them on a file.
86 :
87 : ```plumed
88 : # to see the effect, one could dump the atoms as they were before molecule reconstruction:
89 : # DUMPATOMS FILE=dump-broken.xyz ATOMS=1-20
90 : WHOLEMOLECULES ENTITY0=1-20
91 : DUMPATOMS FILE=dump.xyz ATOMS=1-20
92 : ```
93 :
94 : This command instructs plumed to reconstruct two molecules containing atoms 1-20 and 30-40
95 :
96 : ```plumed
97 : WHOLEMOLECULES ENTITY0=1-20 ENTITY1=30-40
98 : DUMPATOMS FILE=dump.xyz ATOMS=1-20,30-40
99 : ```
100 :
101 : This command instructs plumed to reconstruct the chain of backbone atoms in a
102 : protein
103 :
104 : ```plumed
105 : #SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb
106 : MOLINFO STRUCTURE=regtest/basic/rt32/helix.pdb
107 : WHOLEMOLECULES RESIDUES=all MOLTYPE=protein
108 : ```
109 :
110 : */
111 : //+ENDPLUMEDOC
112 :
113 :
114 : class WholeMolecules:
115 : public ActionPilot,
116 : public ActionAtomistic {
117 : std::vector<std::vector<std::pair<std::size_t,std::size_t> > > p_groups;
118 : std::vector<std::vector<std::pair<std::size_t,std::size_t> > > p_roots;
119 : std::vector<Vector> refs;
120 : bool doemst, addref;
121 : public:
122 : explicit WholeMolecules(const ActionOptions&ao);
123 : static void registerKeywords( Keywords& keys );
124 841 : bool actionHasForces() override {
125 841 : return false;
126 : }
127 : void calculate() override;
128 11946 : void apply() override {}
129 : };
130 :
131 : PLUMED_REGISTER_ACTION(WholeMolecules,"WHOLEMOLECULES")
132 :
133 93 : void WholeMolecules::registerKeywords( Keywords& keys ) {
134 93 : Action::registerKeywords( keys );
135 93 : ActionPilot::registerKeywords( keys );
136 93 : ActionAtomistic::registerKeywords( keys );
137 93 : keys.add("compulsory","STRIDE","1","the frequency with which molecules are reassembled. Unless you are completely certain about what you are doing leave this set equal to 1!");
138 93 : keys.add("numbered","ENTITY","the atoms that make up a molecule that you wish to align. To specify multiple molecules use a list of ENTITY keywords: ENTITY0, ENTITY1,...");
139 186 : keys.reset_style("ENTITY","atoms");
140 93 : keys.add("residues","RESIDUES","this command specifies that the backbone atoms in a set of residues all must be aligned. It must be used in tandem with the \\ref MOLINFO "
141 : "action and the MOLTYPE keyword. If you wish to use all the residues from all the chains in your system you can do so by "
142 : "specifying all. Alternatively, if you wish to use a subset of the residues you can specify the particular residues "
143 : "you are interested in as a list of numbers");
144 93 : keys.add("optional","MOLTYPE","the type of molecule that is under study. This is used to define the backbone atoms");
145 93 : keys.addFlag("EMST", false, "only for backward compatibility, as of PLUMED 2.11 this is the default when using MOLINFO with WHOLE");
146 93 : keys.addFlag("ADDREFERENCE", false, "Define the reference position of the first atom of each entity using a PDB file");
147 93 : keys.addDOI("10.1007/978-1-4939-9608-7_21");
148 93 : }
149 :
150 71 : WholeMolecules::WholeMolecules(const ActionOptions&ao):
151 : Action(ao),
152 : ActionPilot(ao),
153 : ActionAtomistic(ao),
154 71 : doemst(false), addref(false) {
155 : std::vector<std::vector<AtomNumber> > groups;
156 : std::vector<std::vector<AtomNumber> > roots;
157 : // parse optional flags
158 : bool doemst_tmp;
159 71 : parseFlag("EMST", doemst_tmp);
160 71 : if(doemst_tmp) {
161 1 : log << "EMST option is not needed any more as of PLUMED 2.11\n";
162 : }
163 71 : parseFlag("ADDREFERENCE", addref);
164 :
165 71 : auto* moldat=plumed.getActionSet().selectLatest<GenericMolInfo*>(this);
166 :
167 : // create groups from ENTITY
168 422 : for(int i=0;; i++) {
169 : std::vector<AtomNumber> group;
170 986 : parseAtomList("ENTITY",i,group);
171 493 : if( group.empty() ) {
172 : break;
173 : }
174 422 : groups.push_back(group);
175 422 : }
176 :
177 : // Read residues to align from MOLINFO
178 : std::vector<std::string> resstrings;
179 142 : parseVector("RESIDUES",resstrings);
180 71 : if( resstrings.size()>0 ) {
181 0 : if( resstrings.size()==1 ) {
182 0 : if( resstrings[0]=="all" ) {
183 : resstrings[0]="all-ter"; // Include terminal groups in alignment
184 : }
185 : }
186 : std::string moltype;
187 0 : parse("MOLTYPE",moltype);
188 0 : if(moltype.length()==0) {
189 0 : error("Found RESIDUES keyword without specification of the molecule - use MOLTYPE");
190 : }
191 0 : if( !moldat ) {
192 0 : error("MOLINFO is required to use RESIDUES");
193 : }
194 : std::vector< std::vector<AtomNumber> > backatoms;
195 0 : moldat->getBackbone( resstrings, moltype, backatoms );
196 0 : for(unsigned i=0; i<backatoms.size(); ++i) {
197 0 : groups.push_back( backatoms[i] );
198 : }
199 0 : }
200 :
201 : // check number of groups
202 71 : if(groups.size()==0) {
203 0 : error("no atoms found for WHOLEMOLECULES!");
204 : }
205 :
206 : // if using PDBs reorder atoms in groups based on proximity in PDB file
207 71 : if(moldat && moldat->isWhole()) {
208 2 : doemst=true;
209 : }
210 :
211 71 : if(doemst_tmp && ! doemst) {
212 0 : error("cannot enable EMST if MOLINFO is not WHOLE");
213 : }
214 :
215 71 : if(doemst) {
216 2 : if( !moldat ) {
217 0 : error("MOLINFO is required to use EMST");
218 : }
219 : // initialize tree
220 2 : Tree tree = Tree(moldat);
221 : // cycle on groups and reorder atoms
222 4 : for(unsigned i=0; i<groups.size(); ++i) {
223 2 : groups[i] = tree.getTree(groups[i]);
224 : // store root atoms
225 2 : roots.push_back(tree.getRoot());
226 : }
227 2 : } else {
228 : // fill root vector with previous atom in groups
229 489 : for(unsigned i=0; i<groups.size(); ++i) {
230 : std::vector<AtomNumber> root;
231 11390 : for(unsigned j=0; j<groups[i].size()-1; ++j) {
232 10970 : root.push_back(groups[i][j]);
233 : }
234 : // store root atoms
235 420 : roots.push_back(root);
236 : }
237 : }
238 :
239 : // adding reference if needed
240 71 : if(addref) {
241 2 : if( !moldat ) {
242 0 : error("MOLINFO is required to use ADDREFERENCE");
243 : }
244 4 : for(unsigned i=0; i<groups.size(); ++i) {
245 : // add reference position of first atom in entity
246 4 : refs.push_back(moldat->getPosition(groups[i][0]));
247 : }
248 : }
249 :
250 : // print out info
251 493 : for(unsigned i=0; i<groups.size(); ++i) {
252 422 : log.printf(" atoms in entity %d : ",i);
253 12057 : for(unsigned j=0; j<groups[i].size(); ++j) {
254 11635 : log.printf("%d ",groups[i][j].serial() );
255 : }
256 422 : log.printf("\n");
257 422 : if(addref) {
258 2 : log.printf(" with reference position : %lf %lf %lf\n",refs[i][0],refs[i][1],refs[i][2]);
259 : }
260 : }
261 :
262 : // collect all atoms
263 : std::vector<AtomNumber> merge;
264 493 : for(unsigned i=0; i<groups.size(); ++i) {
265 422 : merge.insert(merge.end(),groups[i].begin(),groups[i].end());
266 : }
267 :
268 : // Convert groups to p_groups
269 71 : p_groups.resize( groups.size() );
270 493 : for(unsigned i=0; i<groups.size(); ++i) {
271 422 : p_groups[i].resize( groups[i].size() );
272 12057 : for(unsigned j=0; j<groups[i].size(); ++j) {
273 11635 : p_groups[i][j] = getValueIndices( groups[i][j] );
274 : }
275 : }
276 : // Convert roots to p_roots
277 71 : p_roots.resize( roots.size() );
278 493 : for(unsigned i=0; i<roots.size(); ++i) {
279 422 : p_roots[i].resize( roots[i].size() );
280 11635 : for(unsigned j=0; j<roots[i].size(); ++j) {
281 11213 : p_roots[i][j] = getValueIndices( roots[i][j] );
282 : }
283 : }
284 :
285 :
286 71 : checkRead();
287 71 : Tools::removeDuplicates(merge);
288 71 : requestAtoms(merge);
289 : doNotRetrieve();
290 : doNotForce();
291 71 : }
292 :
293 11946 : void WholeMolecules::calculate() {
294 24596 : for(unsigned i=0; i<p_groups.size(); ++i) {
295 12650 : Vector first = getGlobalPosition(p_groups[i][0]);
296 12650 : if(addref) {
297 12 : first = refs[i]+pbcDistance(refs[i],first);
298 12 : setGlobalPosition( p_groups[i][0], first );
299 : }
300 12650 : if(!doemst) {
301 662472 : for(unsigned j=1; j<p_groups[i].size(); ++j) {
302 649826 : Vector second=getGlobalPosition(p_groups[i][j]);
303 649826 : first = first+pbcDistance(first,second);
304 649826 : setGlobalPosition(p_groups[i][j], first );
305 : }
306 : } else {
307 490 : for(unsigned j=1; j<p_groups[i].size(); ++j) {
308 486 : Vector first=getGlobalPosition(p_roots[i][j-1]);
309 486 : Vector second=getGlobalPosition(p_groups[i][j]);
310 486 : second=first+pbcDistance(first,second);
311 486 : setGlobalPosition(p_groups[i][j], second );
312 : }
313 : }
314 : }
315 11946 : }
316 :
317 :
318 : }
319 : }
|
