[gmx-users] umbrella sample Question

[yujie liu]

Thanks Justin,

What do you means? I have carried out gmx distance to calculate the COM distance between two groups one by one through the previous confxxx.gro by myself, however I never met some fail or warnings. Finally, it seems that I can calculate the distance from all confxxx.gro as well as  your script and just didn’t extract the distance value completely to a text. Can I use a fast method to extract these value?

Please look my summary_distances.dat file
--
0	0.507
1	0.499
2	0.500
3	0.512
4	0.505
5	0.497
6	0.516
7	0.499
8	0.509
9	0.506
10	0.510
11	0.508
12	0.504
13	0.513
14	0.505
15	0.506
16	0.502
17	0.506
18	0.505
19	0.498
20	0.506
21	0.501
22	0.501
23	0.503
24	0.510
25	0.503
26	0.507
27	0.510
28	0.504
29	0.516
30	0.516
31	0.511
32	0.515
33	0.516
34	0.519
35	0.517
36	0.514
37	0.517
38	0.515
39	0.517
40	0.509
41	0.514
42	0.517
43	0.520
44	0.508
45	0.522
46	0.519
47	0.517
48	0.510
49	0.503
50	0.515
51	0.506
52	0.507
53	0.507
54	0.503
55	0.516
56	0.524
57	0.506
58	0.522
59	0.510
60	0.510
61	0.523
62	0.517
63	0.512
64	0.512
65	0.502
66	0.517
67	0.515
68	0.522
69	0.512
70	0.509
71	0.511
72	0.512
73	0.515
74	
75	0.507
76	0.514
77	0.515
78	0.515
79	0.508
80	0.512
81	0.515
82	0.512
83	0.521
84	0.523
85	0.525
86	0.521
87	0.526
88	0.529
89	0.539
90	0.532
91	0.530
92	0.525
93	0.528
94	0.540
95	0.538
96	0.531
97	0.532
98	
99	0.536
100	0.543
101	0.531
102	0.550
103	0.542
104	
105	0.534
106	0.537
107	0.547
108	0.542
109	0.547
110	0.550
111	0.562
112	0.572
113	0.575
114	0.573
115	0.569
116	0.586
117	0.586
118	0.568
119	0.583
120	0.580
121	0.600
122	
123	0.583
124	0.578
125	0.593
126	0.587
127	0.595
128	0.611
129	
130	0.616
131	
132	0.623
133	0.622
134	0.629
135	0.633
136	0.633
137	0.648
138	0.640
139	0.633
140	0.643
141	0.630
142	0.636
143	0.651
144	
145	0.665
146	0.685
147	
148	0.697
149	0.724
150	0.728
151	
152	0.732
153	0.753
154	0.757
155	0.760
156	0.758
157	0.765
158	0.783
159	0.799
160	
161	0.865
162	
163	0.877
164	0.883
165	0.887
166	
167	0.914
168	0.917
169	
170	
171	0.942
172	0.955
173	0.986
174	0.993
175	0.989
176	1.018
177	1.048
178	
179	1.067
180	
181	
182	
183	
184	1.132
185	1.119
186	1.127
187	
188	
189	
190	1.237
191	
192	1.289
193	1.347
194	
195	
196	1.395
197	1.432
198	
199	
200	
201	1.719
202	
203	1.828
204	
205	1.961
206	1.980
207	
208	
209	
210	2.089
211	2.111
212	2.114
213	2.152
214	2.168
215	
216	
217	2.217
218	2.214
219	2.239
220	2.271
221	
222	
223	
224	
225	
226	
227	
228	2.489
229	
230	2.536
231	2.553
232	
233	2.625
234	2.667
235	2.692
236	2.693
237	
238	
239	2.773
240	2.765
241	2.764
242	2.772
243	2.769
244	2.771
245	
246	
247	2.897
248	2.886
249	2.917
250	2.978
251	2.977
252	
253	
254	3.014
255	3.021
256	
257	3.021
258	3.034
259	3.052
260	3.075
261	3.114
262	3.138
263	3.173
264	
265	
266	3.101
267	3.124
268	3.127
269	3.137
270	3.149
271	3.160
272	3.165
273	3.186
274	3.200
275	
276	3.212
277	3.212
278	3.201
279	3.234
280	3.262
281	3.264
282	3.269
283	3.243
284	
285	3.249
286	3.284
287	3.301
288	3.286
289	3.290
290	3.332
291	3.344
292	3.323
293	3.281
294	3.295
295	
296	3.384
297	3.389
298	3.396
299	3.414
300	
301	3.440
302	
303	3.435
304	3.458
305	3.484
306	3.520
307	3.526
308	3.542
309	3.543
310	3.549
311	3.568
312	3.567
313	3.597
314	3.574
315	3.583
316	3.596
317	3.589
318	3.576
319	
320	3.572
321	3.538
322	3.563
323	3.574
324	3.582
325	3.608
326	3.642
327	3.661
328	3.717
329	3.718
330	3.713
331	3.725
332	3.740
333	3.741
334	3.759
335	3.768
336	3.797
337	3.807
338	3.838
339	3.857
340	3.867
341	3.888
342	3.881
343	3.890
344	
345	3.915
346	3.934
347	3.916
348	3.892
349	3.880
350	3.883
351	3.871
352	3.902
353	3.971
354	4.021
355	4.049
356	4.058
357	4.097
358	4.122
359	4.142
360	4.149
361	4.141
362	4.138
363	4.126
364	4.151
365	4.155
366	
367	4.160
368	4.164
369	4.159
370	4.157
371	4.157
372	
373	4.182
374	4.187
375	4.205
376	4.230
377	4.244
378	4.254
379	4.256
380	4.234
381	4.243
382	4.274
383	4.255
384	4.248
385	4.261
386	4.265
387	4.285
388	4.323
389	4.331
390	4.330
391	4.346
392	4.346
393	4.375
394	4.424
395	4.418
396	4.407
397	4.385
398	4.394
399	4.438
400	4.467
401	4.445
402	4.441
403	4.452
404	4.491
405	4.516
406	4.515
407	4.529
408	4.531
409	4.534
410	4.551
411	4.553
412	4.569
413	4.592
414	4.613
415	4.638
416	4.637
417	4.665
418	4.654
419	4.653
420	4.605
421	4.573
422	4.585
423	4.614
424	4.640
425	4.677
426	4.697
427	4.697
428	4.712
429	4.708
430	4.715
431	4.700
432	4.720
433	4.735
434	4.751
435	4.771
436	4.750
437	4.746
438	4.732
439	4.749
440	4.757
441	4.766
442	4.745
443	4.749
444	4.760
445	4.774
446	4.763
447	4.794
448	4.805
449	4.837
450	4.875
451	4.904
452	4.928
453	4.940
454	4.934
455	4.916
456	4.921
457	4.937
458	4.949
459	4.976
460	4.982
461	4.952
462	4.997
463	5.016
464	5.023
465	5.024
466	5.024
467	5.049
468	5.086
469	5.087
470	5.093
471	5.122
472	5.136
473	5.144
474	5.157
475	5.189
476	5.227
477	5.257
478	5.251
479	5.271
480	5.258
481	5.274
482	5.272
483	5.295
484	5.327
485	5.354
486	5.321
487	5.337
488	5.358
489	5.341
490	5.338
491	5.335
492	5.362
493	5.370
494	5.384
495	5.377
496	5.363
497	5.366
498	5.366
499	5.401
500	5.404
--


Thank you

Liu