minimum distance
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rose rahmani
Nov 1, 2021, 11:20:17 AM11/1/21
to PLUMED users
Hi,
I am quite disappointed by how plumed calculates the minimum distance. So I have to calculate the minimum distance between the center of mass of molecule A and any atom of the molecule B(which B in system 1:nanoparticle 2: slab 3: polymer). I have tried the MIN and ALT_MIN functions but both give a very unreasonable distances. I have changes the beta in MIN from 0.1-1 and in ALT_MIN from 10-19 but still the distances (SSD) in COLVAR file are incorrect. Could you please help me?
plumed.dat for MIN function:
Append to existing files
#RESTART
# Flush open files
FLUSH STRIDE=500
# Include file with atom groups
polymer: GROUP NDX_FILE=index.ndx NDX_GROUP=moleculeB
solute: GROUP NDX_FILE=index.ndx NDX_GROUP=moleculeA
# Center of mass of solute and the nearest atom on the surface
solute_COM: COM ATOMS=solute
# Minimum distance between Center of mass of solute and the nearest atom on the surface
d1: DISTANCES GROUPA=solute_COM GROUPB=moleculeB MIN={BETA=0.1}
SSD1: COMBINE ARG=d1.min PERIODIC=NO
d2: DISTANCES GROUPA=solute_COM GROUPB=moleculeB MIN={BETA=0.2}
SSD2: COMBINE ARG=d2.min PERIODIC=NO
d3: DISTANCES GROUPA=solute_COM GROUPB=moleculeB MIN={BETA=0.3}
SSD3: COMBINE ARG=d3.min PERIODIC=NO
d4: DISTANCES GROUPA=solute_COM GROUPB=moleculeB MIN={BETA=0.4}
SSD4: COMBINE ARG=d4.min PERIODIC=NO
d5: DISTANCES GROUPA=solute_COM GROUPB=moleculeB MIN={BETA=0.5}
SSD5: COMBINE ARG=d5.min PERIODIC=NO
d6: DISTANCES GROUPA=solute_COM GROUPB=moleculeB MIN={BETA=0.6}
SSD6: COMBINE ARG=d6.min PERIODIC=NO
d7: DISTANCES GROUPA=solute_COM GROUPB=moleculeB MIN={BETA=0.7}
SSD7: COMBINE ARG=d7.min PERIODIC=NO
d8: DISTANCES GROUPA=solute_COM GROUPB=moleculeB MIN={BETA=0.8}
SSD8: COMBINE ARG=d8.min PERIODIC=NO
d9: DISTANCES GROUPA=solute_COM GROUPB=moleculeB MIN={BETA=0.9}
SSD9: COMBINE ARG=d9.min PERIODIC=NO
d10: DISTANCES GROUPA=solute_COM GROUPB=moleculeB MIN={BETA=1.0}
SSD10: COMBINE ARG=d10.min PERIODIC=NO
# Run metadynamics with grid and multiple walkers
METAD ...
ARG=SSD1
SIGMA=0.05
HEIGHT=0.01
PACE=500
TEMP=300
GRID_MIN=-1
GRID_MAX=2
GRID_BIN=1000
GRID_WSTRIDE=100000
GRID_WFILE=GRID
FILE=HILLS
... METAD
# With an upper wall at 1.5 nm.
uwall: UPPER_WALLS ARG=SSD1 AT=1.5 KAPPA=400000.0 EXP=4 EPS=1.0 OFFSET=0
# Print results
##force: DUMPFORCES ARG=SSD FILE=FORCES
PRINT ARG=SSD1,SSD2,SSD3,SSD4,SSD5,SSD6,SSD7,SSD8,SSD9,SSD10 STRIDE=250 FILE=COLVAR
DUMPFORCES STRIDE=250 ARG=SSD1,SSD2,SSD3,SSD4,SSD5,SSD6,SSD7,SSD8,SSD9,SSD10 FILE=FORCES
------------------------------
#RESTART
# Flush open files
FLUSH STRIDE=500
# Include file with atom groups
polymer: GROUP NDX_FILE=index.ndx NDX_GROUP=moleculeB
solute: GROUP NDX_FILE=index.ndx NDX_GROUP=moleculeA
# Center of mass of solute and the nearest atom on the surface
solute_COM: COM ATOMS=solute
# Minimum distance between Center of mass of solute and the nearest atom on the surface
d1: DISTANCES GROUPA=solute_COM GROUPB=moleculeB MIN={BETA=0.1}
SSD1: COMBINE ARG=d1.min PERIODIC=NO
d2: DISTANCES GROUPA=solute_COM GROUPB=moleculeB MIN={BETA=0.2}
SSD2: COMBINE ARG=d2.min PERIODIC=NO
d3: DISTANCES GROUPA=solute_COM GROUPB=moleculeB MIN={BETA=0.3}
SSD3: COMBINE ARG=d3.min PERIODIC=NO
d4: DISTANCES GROUPA=solute_COM GROUPB=moleculeB MIN={BETA=0.4}
SSD4: COMBINE ARG=d4.min PERIODIC=NO
d5: DISTANCES GROUPA=solute_COM GROUPB=moleculeB MIN={BETA=0.5}
SSD5: COMBINE ARG=d5.min PERIODIC=NO
d6: DISTANCES GROUPA=solute_COM GROUPB=moleculeB MIN={BETA=0.6}
SSD6: COMBINE ARG=d6.min PERIODIC=NO
d7: DISTANCES GROUPA=solute_COM GROUPB=moleculeB MIN={BETA=0.7}
SSD7: COMBINE ARG=d7.min PERIODIC=NO
d8: DISTANCES GROUPA=solute_COM GROUPB=moleculeB MIN={BETA=0.8}
SSD8: COMBINE ARG=d8.min PERIODIC=NO
d9: DISTANCES GROUPA=solute_COM GROUPB=moleculeB MIN={BETA=0.9}
SSD9: COMBINE ARG=d9.min PERIODIC=NO
d10: DISTANCES GROUPA=solute_COM GROUPB=moleculeB MIN={BETA=1.0}
SSD10: COMBINE ARG=d10.min PERIODIC=NO
# Run metadynamics with grid and multiple walkers
METAD ...
ARG=SSD1
SIGMA=0.05
HEIGHT=0.01
PACE=500
TEMP=300
GRID_MIN=-1
GRID_MAX=2
GRID_BIN=1000
GRID_WSTRIDE=100000
GRID_WFILE=GRID
FILE=HILLS
... METAD
# With an upper wall at 1.5 nm.
uwall: UPPER_WALLS ARG=SSD1 AT=1.5 KAPPA=400000.0 EXP=4 EPS=1.0 OFFSET=0
# Print results
##force: DUMPFORCES ARG=SSD FILE=FORCES
PRINT ARG=SSD1,SSD2,SSD3,SSD4,SSD5,SSD6,SSD7,SSD8,SSD9,SSD10 STRIDE=250 FILE=COLVAR
DUMPFORCES STRIDE=250 ARG=SSD1,SSD2,SSD3,SSD4,SSD5,SSD6,SSD7,SSD8,SSD9,SSD10 FILE=FORCES
------------------------------
file plumed.dat for ALT_MIN function is exactly the same except the Beta is from 10-19 in SSD1-SSD10
------------------------------
COLVAR for MIN function
#! FIELDS time SSD1 SSD2 SSD3 SSD4 SSD5 SSD6 SSD7 SSD8 SSD9 SSD10
0.000000 0.024629 0.048186 0.070731 0.092320 0.113006 0.132836 0.151857 0.170110 0.187634 0.204466
0.500000 0.024638 0.048217 0.070798 0.092434 0.113177 0.133071 0.152163 0.170492 0.188096 0.205011
1.000000 0.024634 0.048205 0.070771 0.092386 0.113102 0.132966 0.152021 0.170308 0.187865 0.204727
1.500000 0.024630 0.048186 0.070729 0.092314 0.112992 0.132809 0.151811 0.170038 0.187529 0.204318
2.000000 0.024627 0.048178 0.070713 0.092289 0.112956 0.132763 0.151756 0.169976 0.187461 0.204248
2.500000 0.024640 0.048226 0.070818 0.092469 0.113229 0.133145 0.152261 0.170617 0.188252 0.205199
3.000000 0.024643 0.048239 0.070845 0.092512 0.113290 0.133224 0.152357 0.170728 0.188373 0.205327
3.500000 0.024630 0.048190 0.070737 0.092327 0.113011 0.132837 0.151847 0.170083 0.187582 0.204380
4.000000 0.024628 0.048181 0.070719 0.092298 0.112970 0.132783 0.151781 0.170007 0.187498 0.204291
4.500000 0.024620 0.048151 0.070652 0.092181 0.112791 0.132529 0.151442 0.169571 0.186955 0.203631
5.000000 0.024646 0.048251 0.070872 0.092564 0.113377 0.133356 0.152546 0.170987 0.188715 0.205767
5.500000 0.024645 0.048245 0.070860 0.092543 0.113345 0.133311 0.152485 0.170907 0.188616 0.205646
6.000000 0.024654 0.048282 0.070940 0.092680 0.113551 0.133597 0.152861 0.171382 0.189196 0.206339
6.500000 0.024652 0.048271 0.070915 0.092635 0.113479 0.133492 0.152715 0.171189 0.188948 0.206028
7.000000 0.024661 0.048310 0.071001 0.092786 0.113712 0.133824 0.153163 0.171767 0.189672 0.206913
7.500000 0.024647 0.048253 0.070875 0.092568 0.113379 0.133355 0.152538 0.170969 0.188683 0.205717
8.000000 0.024636 0.048210 0.070783 0.092407 0.113135 0.133011 0.152082 0.170386 0.187962 0.204846
8.500000 0.024628 0.048180 0.070717 0.092292 0.112958 0.132762 0.151748 0.169956 0.187426 0.204193
9.000000 0.024645 0.048246 0.070862 0.092544 0.113342 0.133303 0.152468 0.170878 0.188570 0.205578
9.500000 0.024646 0.048251 0.070870 0.092556 0.113359 0.133322 0.152488 0.170897 0.188584 0.205584
10.000000 0.024652 0.048272 0.070916 0.092636 0.113479 0.133491 0.152711 0.171180 0.188933 0.206004
10.500000 0.024666 0.048329 0.071040 0.092851 0.113808 0.133954 0.153329 0.171972 0.189916 0.207197
11.000000 0.024659 0.048301 0.070979 0.092746 0.113648 0.133728 0.153029 0.171588 0.189442 0.206624
11.500000 0.024624 0.048166 0.070685 0.092237 0.112875 0.132646 0.151596 0.169766 0.187195 0.203919
12.000000 0.024593 0.048047 0.070429 0.091800 0.112219 0.131740 0.150411 0.168278 0.185385 0.201770
12.500000 0.024583 0.048009 0.070346 0.091660 0.112011 0.131453 0.150037 0.167811 0.184819 0.201103
13.000000 0.024588 0.048028 0.070387 0.091730 0.112115 0.131597 0.150226 0.168048 0.185107 0.201443
13.500000 0.024567 0.047946 0.070209 0.091423 0.111648 0.130942 0.149358 0.166943 0.183743 0.199801
14.000000 0.024585 0.048015 0.070360 0.091684 0.112046 0.131501 0.150100 0.167890 0.184914 0.201215
14.500000 0.024582 0.048002 0.070328 0.091625 0.111950 0.131359 0.149901 0.167624 0.184572 0.200784
15.000000 0.024600 0.048071 0.070480 0.091888 0.112352 0.131923 0.150650 0.168579 0.185751 0.202206
15.500000 0.024594 0.048050 0.070434 0.091807 0.112227 0.131744 0.150409 0.168265 0.185356 0.201720
16.000000 0.024590 0.048033 0.070397 0.091743 0.112127 0.131602 0.150217 0.168016 0.185042 0.201333
16.500000 0.024542 0.047847 0.069995 0.091055 0.111095 0.130172 0.148345 0.165663 0.182174 0.197923
17.000000 0.024531 0.047805 0.069897 0.090877 0.110808 0.129749 0.147752 0.164867 0.181139 0.196610
17.500000 0.024511 0.047729 0.069733 0.090598 0.110391 0.129174 0.147002 0.163928 0.179999 0.195260
18.000000 0.024520 0.047763 0.069812 0.090741 0.110617 0.129504 0.147459 0.164534 0.180778 0.196236
18.500000 0.024503 0.047696 0.069661 0.090472 0.110197 0.128896 0.146626 0.163437 0.179378 0.194490
19.000000 0.024473 0.047579 0.069403 0.090022 0.109507 0.127920 0.145320 0.161761 0.177290 0.191953
19.500000 0.024438 0.047443 0.069104 0.089503 0.108712 0.126798 0.143819 0.159829 0.174878 0.189010
20.000000 0.024485 0.047625 0.069505 0.090202 0.109786 0.128320 0.145862 0.162465 0.178177 0.193044
0.000000 0.024629 0.048186 0.070731 0.092320 0.113006 0.132836 0.151857 0.170110 0.187634 0.204466
0.500000 0.024638 0.048217 0.070798 0.092434 0.113177 0.133071 0.152163 0.170492 0.188096 0.205011
1.000000 0.024634 0.048205 0.070771 0.092386 0.113102 0.132966 0.152021 0.170308 0.187865 0.204727
1.500000 0.024630 0.048186 0.070729 0.092314 0.112992 0.132809 0.151811 0.170038 0.187529 0.204318
2.000000 0.024627 0.048178 0.070713 0.092289 0.112956 0.132763 0.151756 0.169976 0.187461 0.204248
2.500000 0.024640 0.048226 0.070818 0.092469 0.113229 0.133145 0.152261 0.170617 0.188252 0.205199
3.000000 0.024643 0.048239 0.070845 0.092512 0.113290 0.133224 0.152357 0.170728 0.188373 0.205327
3.500000 0.024630 0.048190 0.070737 0.092327 0.113011 0.132837 0.151847 0.170083 0.187582 0.204380
4.000000 0.024628 0.048181 0.070719 0.092298 0.112970 0.132783 0.151781 0.170007 0.187498 0.204291
4.500000 0.024620 0.048151 0.070652 0.092181 0.112791 0.132529 0.151442 0.169571 0.186955 0.203631
5.000000 0.024646 0.048251 0.070872 0.092564 0.113377 0.133356 0.152546 0.170987 0.188715 0.205767
5.500000 0.024645 0.048245 0.070860 0.092543 0.113345 0.133311 0.152485 0.170907 0.188616 0.205646
6.000000 0.024654 0.048282 0.070940 0.092680 0.113551 0.133597 0.152861 0.171382 0.189196 0.206339
6.500000 0.024652 0.048271 0.070915 0.092635 0.113479 0.133492 0.152715 0.171189 0.188948 0.206028
7.000000 0.024661 0.048310 0.071001 0.092786 0.113712 0.133824 0.153163 0.171767 0.189672 0.206913
7.500000 0.024647 0.048253 0.070875 0.092568 0.113379 0.133355 0.152538 0.170969 0.188683 0.205717
8.000000 0.024636 0.048210 0.070783 0.092407 0.113135 0.133011 0.152082 0.170386 0.187962 0.204846
8.500000 0.024628 0.048180 0.070717 0.092292 0.112958 0.132762 0.151748 0.169956 0.187426 0.204193
9.000000 0.024645 0.048246 0.070862 0.092544 0.113342 0.133303 0.152468 0.170878 0.188570 0.205578
9.500000 0.024646 0.048251 0.070870 0.092556 0.113359 0.133322 0.152488 0.170897 0.188584 0.205584
10.000000 0.024652 0.048272 0.070916 0.092636 0.113479 0.133491 0.152711 0.171180 0.188933 0.206004
10.500000 0.024666 0.048329 0.071040 0.092851 0.113808 0.133954 0.153329 0.171972 0.189916 0.207197
11.000000 0.024659 0.048301 0.070979 0.092746 0.113648 0.133728 0.153029 0.171588 0.189442 0.206624
11.500000 0.024624 0.048166 0.070685 0.092237 0.112875 0.132646 0.151596 0.169766 0.187195 0.203919
12.000000 0.024593 0.048047 0.070429 0.091800 0.112219 0.131740 0.150411 0.168278 0.185385 0.201770
12.500000 0.024583 0.048009 0.070346 0.091660 0.112011 0.131453 0.150037 0.167811 0.184819 0.201103
13.000000 0.024588 0.048028 0.070387 0.091730 0.112115 0.131597 0.150226 0.168048 0.185107 0.201443
13.500000 0.024567 0.047946 0.070209 0.091423 0.111648 0.130942 0.149358 0.166943 0.183743 0.199801
14.000000 0.024585 0.048015 0.070360 0.091684 0.112046 0.131501 0.150100 0.167890 0.184914 0.201215
14.500000 0.024582 0.048002 0.070328 0.091625 0.111950 0.131359 0.149901 0.167624 0.184572 0.200784
15.000000 0.024600 0.048071 0.070480 0.091888 0.112352 0.131923 0.150650 0.168579 0.185751 0.202206
15.500000 0.024594 0.048050 0.070434 0.091807 0.112227 0.131744 0.150409 0.168265 0.185356 0.201720
16.000000 0.024590 0.048033 0.070397 0.091743 0.112127 0.131602 0.150217 0.168016 0.185042 0.201333
16.500000 0.024542 0.047847 0.069995 0.091055 0.111095 0.130172 0.148345 0.165663 0.182174 0.197923
17.000000 0.024531 0.047805 0.069897 0.090877 0.110808 0.129749 0.147752 0.164867 0.181139 0.196610
17.500000 0.024511 0.047729 0.069733 0.090598 0.110391 0.129174 0.147002 0.163928 0.179999 0.195260
18.000000 0.024520 0.047763 0.069812 0.090741 0.110617 0.129504 0.147459 0.164534 0.180778 0.196236
18.500000 0.024503 0.047696 0.069661 0.090472 0.110197 0.128896 0.146626 0.163437 0.179378 0.194490
19.000000 0.024473 0.047579 0.069403 0.090022 0.109507 0.127920 0.145320 0.161761 0.177290 0.191953
19.500000 0.024438 0.047443 0.069104 0.089503 0.108712 0.126798 0.143819 0.159829 0.174878 0.189010
20.000000 0.024485 0.047625 0.069505 0.090202 0.109786 0.128320 0.145862 0.162465 0.178177 0.193044
real distances calculated by MDanalysis:
0.711076637594801
0.686211580552166
0.643828429356176
0.655394676722033
0.639169102386638
0.672585658402185
0.666359931603232
0.611693866272018
0.628466182696358
0.642281231862288
0.756539844889028
0.746638555494146
0.732929577401778
0.693738515204775
0.743420376680012
0.685330966523793
0.657062601540277
0.624187035718232
0.652108767605284
0.669640830575903
0.671257535300613
0.746591914567469
0.725660027643153
0.635305057080758
0.687070000700232
0.679291004874519
0.679411399190305
0.59069640811742
0.670761632997759
0.658171511320518
0.698035017031904
0.602673033689062
0.569681502117849
0.530175473723929
0.462883540226044
0.458177848776518
0.488587267795363
0.424275042905893
0.41243058215892
0.360551202649313
0.416974544258247
----------------------------
COLVAR file for ALT_MIN function
#! FIELDS time SSD1 SSD2 SSD3 SSD4 SSD5 SSD6 SSD7 SSD8 SSD9 SSD10
0.000000 0.549416 0.574347 0.594329 0.610592 0.623999 0.635173 0.644572 0.652541 0.659344 0.665188
0.500000 0.554333 0.578357 0.597466 0.612895 0.625507 0.635927 0.644610 0.651901 0.658064 0.663301
1.000000 0.558022 0.580389 0.597792 0.611502 0.622412 0.631165 0.638236 0.643982 0.648673 0.652519
1.500000 0.557384 0.581690 0.601063 0.616729 0.629546 0.640135 0.648952 0.656342 0.662570 0.667842
2.000000 0.539867 0.564083 0.583282 0.598719 0.611272 0.621577 0.630102 0.637200 0.643142 0.648137
2.500000 0.478907 0.503853 0.523868 0.540183 0.553660 0.564919 0.574418 0.582501 0.589432 0.595414
3.000000 0.482584 0.507322 0.527213 0.543460 0.556905 0.568154 0.577652 0.585735 0.592660 0.598627
3.500000 0.498742 0.523470 0.543426 0.559812 0.573464 0.584982 0.594804 0.603261 0.610604 0.617026
4.000000 0.469489 0.493470 0.512606 0.528107 0.540820 0.551354 0.560159 0.567572 0.573851 0.579198
4.500000 0.466318 0.490720 0.510180 0.525934 0.538850 0.549549 0.558494 0.566030 0.572421 0.577874
5.000000 0.479990 0.504897 0.524873 0.541152 0.554599 0.565838 0.575326 0.583405 0.590339 0.596332
5.500000 0.461869 0.485713 0.504724 0.520117 0.532743 0.543212 0.551976 0.559373 0.565662 0.571043
6.000000 0.478155 0.502141 0.521289 0.536812 0.549556 0.560132 0.568988 0.576462 0.582811 0.588237
6.500000 0.507557 0.532648 0.552875 0.569451 0.583227 0.594811 0.604654 0.613090 0.620377 0.626714
7.000000 0.554502 0.579496 0.599427 0.615548 0.628738 0.639634 0.648706 0.656309 0.662717 0.668141
7.500000 0.558463 0.578592 0.594009 0.605986 0.615406 0.622896 0.628907 0.633771 0.637736 0.640988
8.000000 0.612665 0.636664 0.655628 0.670802 0.683063 0.693046 0.701223 0.707951 0.713507 0.718108
8.500000 0.573743 0.598406 0.618205 0.634354 0.647704 0.658866 0.668289 0.676312 0.683192 0.689130
9.000000 0.611399 0.636454 0.656602 0.673060 0.686680 0.698080 0.707711 0.715915 0.722955 0.729035
9.500000 0.622490 0.646971 0.666596 0.682579 0.695772 0.706785 0.716068 0.723960 0.730719 0.736545
10.000000 0.663934 0.688441 0.708069 0.724037 0.737197 0.748166 0.757394 0.765224 0.771914 0.777668
10.500000 0.629660 0.653821 0.673146 0.688847 0.701772 0.712529 0.721565 0.729218 0.735742 0.741340
11.000000 0.637746 0.662878 0.683105 0.699652 0.713376 0.724892 0.734655 0.743005 0.750201 0.756446
11.500000 0.545921 0.570157 0.589622 0.605508 0.618644 0.629630 0.638905 0.646800 0.653569 0.659409
12.000000 0.572249 0.596823 0.616538 0.632612 0.645897 0.657007 0.666393 0.674394 0.681267 0.687215
12.500000 0.587088 0.612005 0.632018 0.648345 0.661838 0.673113 0.682622 0.690706 0.697629 0.703592
13.000000 0.539198 0.564947 0.585752 0.602836 0.617056 0.629030 0.639213 0.647951 0.655505 0.662082
13.500000 0.560561 0.585325 0.605252 0.621547 0.635052 0.646374 0.655960 0.664147 0.671191 0.677293
14.000000 0.563397 0.588729 0.609173 0.625942 0.639885 0.651615 0.661583 0.670129 0.677514 0.683941
14.500000 0.553638 0.578825 0.599145 0.615799 0.629628 0.641236 0.651070 0.659466 0.666683 0.672921
15.000000 0.598250 0.623243 0.643356 0.659793 0.673397 0.684777 0.694382 0.702551 0.709546 0.715570
15.500000 0.615440 0.639029 0.657840 0.673084 0.685608 0.696020 0.704767 0.712186 0.718531 0.723999
16.000000 0.637262 0.662009 0.681892 0.698125 0.711562 0.722813 0.732331 0.740456 0.747446 0.753504
16.500000 0.704454 0.728377 0.747500 0.763036 0.775834 0.786504 0.795493 0.803137 0.809693 0.815358
17.000000 0.691167 0.715255 0.734637 0.750489 0.763635 0.774666 0.784020 0.792024 0.798929 0.804931
17.500000 0.727344 0.751145 0.770119 0.785476 0.798061 0.808486 0.817200 0.824540 0.830767 0.836080
18.000000 0.721093 0.745870 0.765805 0.782102 0.795608 0.806929 0.816514 0.824701 0.831747 0.837854
18.500000 0.698742 0.721192 0.738963 0.753253 0.764901 0.774507 0.782511 0.789242 0.794948 0.799823
19.000000 0.665273 0.687665 0.705428 0.719763 0.731506 0.741252 0.749436 0.756382 0.762335 0.767480
19.500000 0.620310 0.641349 0.657915 0.671203 0.682040 0.691010 0.698535 0.704925 0.710414 0.715176
20.000000 0.568207 0.590601 0.608345 0.622647 0.634346 0.644044 0.652178 0.659074 0.664978 0.670078
0.000000 0.549416 0.574347 0.594329 0.610592 0.623999 0.635173 0.644572 0.652541 0.659344 0.665188
0.500000 0.554333 0.578357 0.597466 0.612895 0.625507 0.635927 0.644610 0.651901 0.658064 0.663301
1.000000 0.558022 0.580389 0.597792 0.611502 0.622412 0.631165 0.638236 0.643982 0.648673 0.652519
1.500000 0.557384 0.581690 0.601063 0.616729 0.629546 0.640135 0.648952 0.656342 0.662570 0.667842
2.000000 0.539867 0.564083 0.583282 0.598719 0.611272 0.621577 0.630102 0.637200 0.643142 0.648137
2.500000 0.478907 0.503853 0.523868 0.540183 0.553660 0.564919 0.574418 0.582501 0.589432 0.595414
3.000000 0.482584 0.507322 0.527213 0.543460 0.556905 0.568154 0.577652 0.585735 0.592660 0.598627
3.500000 0.498742 0.523470 0.543426 0.559812 0.573464 0.584982 0.594804 0.603261 0.610604 0.617026
4.000000 0.469489 0.493470 0.512606 0.528107 0.540820 0.551354 0.560159 0.567572 0.573851 0.579198
4.500000 0.466318 0.490720 0.510180 0.525934 0.538850 0.549549 0.558494 0.566030 0.572421 0.577874
5.000000 0.479990 0.504897 0.524873 0.541152 0.554599 0.565838 0.575326 0.583405 0.590339 0.596332
5.500000 0.461869 0.485713 0.504724 0.520117 0.532743 0.543212 0.551976 0.559373 0.565662 0.571043
6.000000 0.478155 0.502141 0.521289 0.536812 0.549556 0.560132 0.568988 0.576462 0.582811 0.588237
6.500000 0.507557 0.532648 0.552875 0.569451 0.583227 0.594811 0.604654 0.613090 0.620377 0.626714
7.000000 0.554502 0.579496 0.599427 0.615548 0.628738 0.639634 0.648706 0.656309 0.662717 0.668141
7.500000 0.558463 0.578592 0.594009 0.605986 0.615406 0.622896 0.628907 0.633771 0.637736 0.640988
8.000000 0.612665 0.636664 0.655628 0.670802 0.683063 0.693046 0.701223 0.707951 0.713507 0.718108
8.500000 0.573743 0.598406 0.618205 0.634354 0.647704 0.658866 0.668289 0.676312 0.683192 0.689130
9.000000 0.611399 0.636454 0.656602 0.673060 0.686680 0.698080 0.707711 0.715915 0.722955 0.729035
9.500000 0.622490 0.646971 0.666596 0.682579 0.695772 0.706785 0.716068 0.723960 0.730719 0.736545
10.000000 0.663934 0.688441 0.708069 0.724037 0.737197 0.748166 0.757394 0.765224 0.771914 0.777668
10.500000 0.629660 0.653821 0.673146 0.688847 0.701772 0.712529 0.721565 0.729218 0.735742 0.741340
11.000000 0.637746 0.662878 0.683105 0.699652 0.713376 0.724892 0.734655 0.743005 0.750201 0.756446
11.500000 0.545921 0.570157 0.589622 0.605508 0.618644 0.629630 0.638905 0.646800 0.653569 0.659409
12.000000 0.572249 0.596823 0.616538 0.632612 0.645897 0.657007 0.666393 0.674394 0.681267 0.687215
12.500000 0.587088 0.612005 0.632018 0.648345 0.661838 0.673113 0.682622 0.690706 0.697629 0.703592
13.000000 0.539198 0.564947 0.585752 0.602836 0.617056 0.629030 0.639213 0.647951 0.655505 0.662082
13.500000 0.560561 0.585325 0.605252 0.621547 0.635052 0.646374 0.655960 0.664147 0.671191 0.677293
14.000000 0.563397 0.588729 0.609173 0.625942 0.639885 0.651615 0.661583 0.670129 0.677514 0.683941
14.500000 0.553638 0.578825 0.599145 0.615799 0.629628 0.641236 0.651070 0.659466 0.666683 0.672921
15.000000 0.598250 0.623243 0.643356 0.659793 0.673397 0.684777 0.694382 0.702551 0.709546 0.715570
15.500000 0.615440 0.639029 0.657840 0.673084 0.685608 0.696020 0.704767 0.712186 0.718531 0.723999
16.000000 0.637262 0.662009 0.681892 0.698125 0.711562 0.722813 0.732331 0.740456 0.747446 0.753504
16.500000 0.704454 0.728377 0.747500 0.763036 0.775834 0.786504 0.795493 0.803137 0.809693 0.815358
17.000000 0.691167 0.715255 0.734637 0.750489 0.763635 0.774666 0.784020 0.792024 0.798929 0.804931
17.500000 0.727344 0.751145 0.770119 0.785476 0.798061 0.808486 0.817200 0.824540 0.830767 0.836080
18.000000 0.721093 0.745870 0.765805 0.782102 0.795608 0.806929 0.816514 0.824701 0.831747 0.837854
18.500000 0.698742 0.721192 0.738963 0.753253 0.764901 0.774507 0.782511 0.789242 0.794948 0.799823
19.000000 0.665273 0.687665 0.705428 0.719763 0.731506 0.741252 0.749436 0.756382 0.762335 0.767480
19.500000 0.620310 0.641349 0.657915 0.671203 0.682040 0.691010 0.698535 0.704925 0.710414 0.715176
20.000000 0.568207 0.590601 0.608345 0.622647 0.634346 0.644044 0.652178 0.659074 0.664978 0.670078
real distances calculated by MD analysis:
0.549416
0.554333
0.558022
0.557384
0.539867
0.478907
0.482584
0.498742
0.469489
0.466318
0.47999
0.461869
0.478155
0.507557
0.554502
0.558463
0.612665
0.573743
0.611399
0.62249
0.663934
0.62966
0.637746
0.545921
0.572249
0.587088
0.539198
0.560561
0.563397
0.553638
0.59825
0.61544
0.637262
0.704454
0.691167
0.727344
0.721093
0.698742
0.665273
0.62031
0.568207
Best,
Rose
Gareth Tribello
Nov 1, 2021, 11:26:48 AM11/1/21
to plumed...@googlegroups.com
There are two ways to proceed.
(1) Set BETA much larger — think 10.
Or
(2) Use LOWEST instead of MIN. That will give you the shortest of the distances you are calculating. There is a discontinuity in the derivatives when you use this method (which is why people have traditionally used the formula that is used with MIN). This discontinuity doesn’t really matter in the grand scheme of things.
I hope this helps
Gareth
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roja rahmani
Nov 1, 2021, 1:42:52 PM11/1/21
to PLUMED users
Hi,
Thank you so much. Do you mean this?
# Append to existing files
#RESTART
# Flush open files
FLUSH STRIDE=500
# Include file with atom groups
PMMA: GROUP NDX_FILE=index.ndx NDX_GROUP=PMMA
solute: GROUP NDX_FILE=index.ndx NDX_GROUP=ASP
solute: GROUP NDX_FILE=index.ndx NDX_GROUP=ASP
# Center of mass of solute and the nearest atom on the surface
solute_COM: COM ATOMS=solute
# Minimum distance between Center of mass of solute and the nearest atom on the surface
d: DISTANCES GROUPA=solute_COM GROUPB=PMMA LOWEST
SSD: COMBINE ARG=d.lowest PERIODIC=NO
SSD: COMBINE ARG=d.lowest PERIODIC=NO
# Run metadynamics with grid and multiple walkers
METAD ...
ARG=SSD
SIGMA=0.05
HEIGHT=0.01
PACE=500
TEMP=300
GRID_MIN=-1
GRID_MAX=2
GRID_BIN=1000
GRID_WSTRIDE=100000
GRID_WFILE=GRID
FILE=HILLS
... METAD
# With an upper wall at 1.5 nm.
HEIGHT=0.01
PACE=500
TEMP=300
GRID_MIN=-1
GRID_MAX=2
GRID_BIN=1000
GRID_WSTRIDE=100000
GRID_WFILE=GRID
FILE=HILLS
... METAD
# With an upper wall at 1.5 nm.
uwall: UPPER_WALLS ARG=SSD AT=1.5 KAPPA=400000.0 EXP=4 EPS=1.0 OFFSET=0
# Print results
##force: DUMPFORCES ARG=SSD FILE=FORCES
PRINT ARG=SSD STRIDE=250 FILE=COLVAR
DUMPFORCES STRIDE=250 ARG=SSD FILE=FORCES
----------------
DUMPFORCES STRIDE=250 ARG=SSD FILE=FORCES
----------------
And I didn't understand what do you mean by "discontinuity". I have one more question. So I have some data calculated by ALT_MIN. Is there any way to correct these distances calculated by AL distances to the dsddsfsT_MIN? and convert it to the LOWEST values. Is there any particular shift that I could use to convert and correct those wrong distances without running new calculation by LOWEST?
Best,
Roja
Gareth Tribello
Nov 1, 2021, 2:30:49 PM11/1/21
to plumed...@googlegroups.com
Hello again
That input is exactly what I mean.
Discontinuities are described here:
The issue here is at the point when the identity of the closest atom changes. At that point one atom will stop experiencing any force and another will start feeling the force. In practise this is a not a real problem. If the value of the CV changes discontinuously that is a big problem but it is only the derivatives that change discontinuously here so it doesn’t matter.
in answer to your final question the answer is no you cannot calculate recalculate the distances if you only have the value of the alt min. What you are asking here is if you can calculate N unknowns from one equation.
Good luck
Gareth
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roja rahmani
Nov 1, 2021, 2:46:21 PM11/1/21
to PLUMED users
So this will not change the PMF and the free energy value even though the distances are not correct?
Roja
Gareth Tribello
Nov 1, 2021, 2:53:00 PM11/1/21
to plumed...@googlegroups.com
Well, the free energy surface will change if the CV you are using changes. Not sure I understand the question.
Gareth
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