-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathAssertion failed.log
360 lines (320 loc) · 17.5 KB
/
Assertion failed.log
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
:-) GROMACS - gmx grompp, 2019.3 (-:
GROMACS is written by:
Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
Christian Wennberg Maarten Wolf
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2018, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS: gmx grompp, version 2019.3
Executable: /shared/ucl/apps/gromacs/2019.3/intel-2018/bin/gmx
Data prefix: /shared/ucl/apps/gromacs/2019.3/intel-2018
Working dir: /lustre/scratch/scratch/ucbechz/20191108_REMD_tutorial/tutorial-archive/stage2/sim0
Command line:
gmx grompp -f sim -c confout -t equil-state
Ignoring obsolete mdp entry 'optimize-fft'
Ignoring obsolete mdp entry 'rlistlong'
Ignoring obsolete mdp entry 'nstcalclr'
Ignoring obsolete mdp entry 'gb-algorithm'
Ignoring obsolete mdp entry 'nstgbradii'
Ignoring obsolete mdp entry 'rgbradii'
Ignoring obsolete mdp entry 'gb-epsilon-solvent'
Ignoring obsolete mdp entry 'gb-saltconc'
Ignoring obsolete mdp entry 'gb-obc-alpha'
Ignoring obsolete mdp entry 'gb-obc-beta'
Ignoring obsolete mdp entry 'gb-obc-gamma'
Ignoring obsolete mdp entry 'gb-dielectric-offset'
Ignoring obsolete mdp entry 'sa-algorithm'
Ignoring obsolete mdp entry 'sa-surface-tension'
Replacing old mdp entry 'verlet-buffer-drift' by 'verlet-buffer-tolerance'
Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'
Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'
Generated 20503 of the 20503 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 17396 of the 20503 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein'
Excluding 2 bonded neighbours molecule type 'SOL'
NOTE 1 [file unknown]:
You are using constraints on all bonds, whereas the forcefield has been
parametrized only with constraints involving hydrogen atoms. We suggest
using constraints = h-bonds instead, this will also improve performance.
Removing all charge groups because cutoff-scheme=Verlet
Number of degrees of freedom in T-Coupling group System is 2742.00
Reading Coordinates, Velocities and Box size from old trajectory
Will read whole trajectory
-------------------------------------------------------
Program: gmx grompp, version 2019.3
Source file: src/gromacs/fileio/checkpoint.cpp (line 591)
Function: lambda []()->auto::operator()()->auto
Assertion failed:
Condition: list != nullptr || (v != nullptr && vector == nullptr) || (v == nullptr && vector != nullptr)
Without list, we should have exactly one of v and vector != NULL
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
turning all bonds into constraints...
turning all bonds into constraints...
Analysing residue names:
There are: 3 Protein residues
There are: 450 Water residues
Analysing Protein...
Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 298 K
Calculated rlist for 1x1 atom pair-list as 1.035 nm, buffer size 0.035 nm
Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
Note that mdrun will redetermine rlist based on the actual pair-list setup
:-) GROMACS - gmx grompp, 2019.3 (-:
GROMACS is written by:
Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
Christian Wennberg Maarten Wolf
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2018, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS: gmx grompp, version 2019.3
Executable: /shared/ucl/apps/gromacs/2019.3/intel-2018/bin/gmx
Data prefix: /shared/ucl/apps/gromacs/2019.3/intel-2018
Working dir: /lustre/scratch/scratch/ucbechz/20191108_REMD_tutorial/tutorial-archive/stage2/sim1
Command line:
gmx grompp -f sim -c confout -t equil-state
Ignoring obsolete mdp entry 'optimize-fft'
Ignoring obsolete mdp entry 'rlistlong'
Ignoring obsolete mdp entry 'nstcalclr'
Ignoring obsolete mdp entry 'gb-algorithm'
Ignoring obsolete mdp entry 'nstgbradii'
Ignoring obsolete mdp entry 'rgbradii'
Ignoring obsolete mdp entry 'gb-epsilon-solvent'
Ignoring obsolete mdp entry 'gb-saltconc'
Ignoring obsolete mdp entry 'gb-obc-alpha'
Ignoring obsolete mdp entry 'gb-obc-beta'
Ignoring obsolete mdp entry 'gb-obc-gamma'
Ignoring obsolete mdp entry 'gb-dielectric-offset'
Ignoring obsolete mdp entry 'sa-algorithm'
Ignoring obsolete mdp entry 'sa-surface-tension'
Replacing old mdp entry 'verlet-buffer-drift' by 'verlet-buffer-tolerance'
Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'
Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'
Generated 20503 of the 20503 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 17396 of the 20503 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein'
Excluding 2 bonded neighbours molecule type 'SOL'
NOTE 1 [file unknown]:
You are using constraints on all bonds, whereas the forcefield has been
parametrized only with constraints involving hydrogen atoms. We suggest
using constraints = h-bonds instead, this will also improve performance.
Removing all charge groups because cutoff-scheme=Verlet
Number of degrees of freedom in T-Coupling group System is 2742.00
Reading Coordinates, Velocities and Box size from old trajectory
Will read whole trajectory
-------------------------------------------------------
Program: gmx grompp, version 2019.3
Source file: src/gromacs/fileio/checkpoint.cpp (line 591)
Function: lambda []()->auto::operator()()->auto
Assertion failed:
Condition: list != nullptr || (v != nullptr && vector == nullptr) || (v == nullptr && vector != nullptr)
Without list, we should have exactly one of v and vector != NULL
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
turning all bonds into constraints...
turning all bonds into constraints...
Analysing residue names:
There are: 3 Protein residues
There are: 450 Water residues
Analysing Protein...
Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 308 K
Calculated rlist for 1x1 atom pair-list as 1.036 nm, buffer size 0.036 nm
Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
Note that mdrun will redetermine rlist based on the actual pair-list setup
:-) GROMACS - gmx grompp, 2019.3 (-:
GROMACS is written by:
Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
Christian Wennberg Maarten Wolf
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2018, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS: gmx grompp, version 2019.3
Executable: /shared/ucl/apps/gromacs/2019.3/intel-2018/bin/gmx
Data prefix: /shared/ucl/apps/gromacs/2019.3/intel-2018
Working dir: /lustre/scratch/scratch/ucbechz/20191108_REMD_tutorial/tutorial-archive/stage2/sim2
Command line:
gmx grompp -f sim -c confout -t equil-state
Ignoring obsolete mdp entry 'optimize-fft'
Ignoring obsolete mdp entry 'rlistlong'
Ignoring obsolete mdp entry 'nstcalclr'
Ignoring obsolete mdp entry 'gb-algorithm'
Ignoring obsolete mdp entry 'nstgbradii'
Ignoring obsolete mdp entry 'rgbradii'
Ignoring obsolete mdp entry 'gb-epsilon-solvent'
Ignoring obsolete mdp entry 'gb-saltconc'
Ignoring obsolete mdp entry 'gb-obc-alpha'
Ignoring obsolete mdp entry 'gb-obc-beta'
Ignoring obsolete mdp entry 'gb-obc-gamma'
Ignoring obsolete mdp entry 'gb-dielectric-offset'
Ignoring obsolete mdp entry 'sa-algorithm'
Ignoring obsolete mdp entry 'sa-surface-tension'
Replacing old mdp entry 'verlet-buffer-drift' by 'verlet-buffer-tolerance'
Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'
Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'
Generated 20503 of the 20503 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 17396 of the 20503 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein'
Excluding 2 bonded neighbours molecule type 'SOL'
NOTE 1 [file unknown]:
You are using constraints on all bonds, whereas the forcefield has been
parametrized only with constraints involving hydrogen atoms. We suggest
using constraints = h-bonds instead, this will also improve performance.
Removing all charge groups because cutoff-scheme=Verlet
Number of degrees of freedom in T-Coupling group System is 2742.00
Reading Coordinates, Velocities and Box size from old trajectory
Will read whole trajectory
-------------------------------------------------------
Program: gmx grompp, version 2019.3
Source file: src/gromacs/fileio/checkpoint.cpp (line 591)
Function: lambda []()->auto::operator()()->auto
Assertion failed:
Condition: list != nullptr || (v != nullptr && vector == nullptr) || (v == nullptr && vector != nullptr)
Without list, we should have exactly one of v and vector != NULL
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
turning all bonds into constraints...
turning all bonds into constraints...
Analysing residue names:
There are: 3 Protein residues
There are: 450 Water residues
Analysing Protein...
Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 318.34 K
Calculated rlist for 1x1 atom pair-list as 1.037 nm, buffer size 0.037 nm
Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
Note that mdrun will redetermine rlist based on the actual pair-list setup
:-) GROMACS - gmx grompp, 2019.3 (-:
GROMACS is written by:
Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
Christian Wennberg Maarten Wolf
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2018, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS: gmx grompp, version 2019.3
Executable: /shared/ucl/apps/gromacs/2019.3/intel-2018/bin/gmx
Data prefix: /shared/ucl/apps/gromacs/2019.3/intel-2018
Working dir: /lustre/scratch/scratch/ucbechz/20191108_REMD_tutorial/tutorial-archive/stage2/sim3
Command line:
gmx grompp -f sim -c confout -t equil-state
Ignoring obsolete mdp entry 'optimize-fft'
Ignoring obsolete mdp entry 'rlistlong'
Ignoring obsolete mdp entry 'nstcalclr'
Ignoring obsolete mdp entry 'gb-algorithm'
Ignoring obsolete mdp entry 'nstgbradii'
Ignoring obsolete mdp entry 'rgbradii'
Ignoring obsolete mdp entry 'gb-epsilon-solvent'
Ignoring obsolete mdp entry 'gb-saltconc'
Ignoring obsolete mdp entry 'gb-obc-alpha'
Ignoring obsolete mdp entry 'gb-obc-beta'
Ignoring obsolete mdp entry 'gb-obc-gamma'
Ignoring obsolete mdp entry 'gb-dielectric-offset'
Ignoring obsolete mdp entry 'sa-algorithm'
Ignoring obsolete mdp entry 'sa-surface-tension'
Replacing old mdp entry 'verlet-buffer-drift' by 'verlet-buffer-tolerance'
Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'
Replacing old mdp entry 'xtc-precision' by 'compressed-x-precision'
Generated 20503 of the 20503 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 17396 of the 20503 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein'
Excluding 2 bonded neighbours molecule type 'SOL'
NOTE 1 [file unknown]:
You are using constraints on all bonds, whereas the forcefield has been
parametrized only with constraints involving hydrogen atoms. We suggest
using constraints = h-bonds instead, this will also improve performance.
Removing all charge groups because cutoff-scheme=Verlet
Number of degrees of freedom in T-Coupling group System is 2742.00
Reading Coordinates, Velocities and Box size from old trajectory
Will read whole trajectory
-------------------------------------------------------
Program: gmx grompp, version 2019.3
Source file: src/gromacs/fileio/checkpoint.cpp (line 591)
Function: lambda []()->auto::operator()()->auto
Assertion failed:
Condition: list != nullptr || (v != nullptr && vector == nullptr) || (v == nullptr && vector != nullptr)
Without list, we should have exactly one of v and vector != NULL
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
turning all bonds into constraints...
turning all bonds into constraints...
Analysing residue names:
There are: 3 Protein residues
There are: 450 Water residues
Analysing Protein...
Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 329.02 K
Calculated rlist for 1x1 atom pair-list as 1.038 nm, buffer size 0.038 nm
Set rlist, assuming 4x4 atom pair-list, to 1.000 nm, buffer size 0.000 nm
Note that mdrun will redetermine rlist based on the actual pair-list setup