[gmx-users] problem caused by removed [ pairs ] in OPLS
Rongliang Wu
wurl04 at iccas.ac.cn
Wed Apr 5 10:48:12 CEST 2006
Hello, gmx-users，
i've met with a problem whem simulating just a single peo molecule using OPLS, I deleted the [ pairs ] part because in mannual 3.2 page 103 there is
"If you want to include Ryckaert-Bellemans type
dihedrals in a topology, do the following (in case of e.g. decane):
[ dihedrals ]
; ai aj ak al funct c0 c1 c2
1 2 3 4 3
2 3 4 5 3
and do not forget to erase the 1-4 interaction in [ pairs ]!!"
and my simulation ended with
"Step 867, time 1.734 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max 22942626521022464.000000 (between atoms 40 and 41) rms 10117857396391936.000000
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1 2 178.5 657957847040.0000 3977670819840.0000 0.1090
1 3 178.5 657957847040.0000 3977670819840.0000 0.1090
1 4 178.5 657957847040.0000 3977670819840.0000 0.1090
1 5 178.6 1416787918848.0000 8551896973312.0000 0.1529
5 6 178.5 1757728735232.0000 10609417519104.0000 0.1090
5 7 178.5 1757728735232.0000 10609417519104.0000 0.1090
5 8 178.7 2308053401600.0000 13921285046272.0000 0.1410
8 9 179.0 4335363948544.0000 26209574453248.0000 0.1410
9 10 179.0 5223166246912.0000 31550504697856.0000 0.1090
9 11 179.0 5223166246912.0000 31550508892160.0000 0.1090
9 12 179.2 7040408748032.0000 43108314120192.0000 0.1529
12 13 179.3 6815090212864.0000 41816460099584.0000 0.1090
12 14 179.3 6815090212864.0000 41816455905280.0000 0.1090
12 15 179.3 7502266105856.0000 47497573564416.0000 0.1410
15 16 179.1 10733254344704.0000 73381714067456.0000 0.1410
16 17 179.1 12365224476672.0000 85125429723136.0000 0.1090
16 18 179.1 12365225525248.0000 85125421334528.0000 0.1090
16 19 178.9 15856216047616.0000 119592206729216.0000 0.1529
19 20 179.0 14840055726080.0000 115651775561728.0000 0.1090
19 21 179.0 14840055726080.0000 115651775561728.0000 0.1090
19 22 178.6 15600420126720.0000 139935948472320.0000 0.1410
22 23 179.0 20373087191040.0000 242612669775872.0000 0.1410
23 24 179.5 23078771884032.0000 286189374406656.0000 0.1090
23 25 179.5 23078771884032.0000 286189374406656.0000 0.1090
23 26 179.1 28774722699264.0000 421234454036480.0000 0.1529
26 27 179.5 26472026734592.0000 418777766297600.0000 0.1090
26 28 179.5 26472026734592.0000 418777766297600.0000 0.1090
26 29 178.9 26974797955072.0000 511880510570496.0000 0.1410
29 30 179.6 32810710597632.0000 875089654448128.0000 0.1410
30 31 179.8 36556526059520.0000 1039885737656320.0000 0.1090
30 32 179.8 36556526059520.0000 1039885737656320.0000 0.1090
30 33 179.8 44349714857984.0000 1405206327721984.0000 0.1529
33 34 179.9 39958215655424.0000 1360967627702272.0000 0.1090
33 35 179.9 39958215655424.0000 1360967627702272.0000 0.1090
33 36 179.7 39353413795840.0000 1475370658299904.0000 0.1410
36 37 179.9 43549164830720.0000 2011543101243392.0000 0.1410
37 38 179.9 47245537837056.0000 2307230393171968.0000 0.1090
37 39 179.9 47245537837056.0000 2307230393171968.0000 0.1090
37 40 180.0 55497927426048.0000 2763734682435584.0000 0.1529
40 41 179.9 48634812956672.0000 2500746318708736.0000 0.1090
40 42 179.9 48634812956672.0000 2500746318708736.0000 0.1090
40 43 180.0 46185549135872.0000 2357986169192448.0000 0.1410
43 44 179.9 45946540916736.0000 2302985086435328.0000 0.1410
44 45 179.9 48239311060992.0000 2404420939677696.0000 0.1090
44 46 179.9 48239311060992.0000 2404420939677696.0000 0.1090
44 47 179.9 54781926178816.0000 2621617704271872.0000 0.1529
47 48 179.8 46453888122880.0000 2153688130912256.0000 0.1090
47 49 179.8 46453888122880.0000 2153688130912256.0000 0.1090
47 50 179.9 42475469144064.0000 1850107494400000.0000 0.1410
50 51 179.6 37316882071552.0000 1267195740946432.0000 0.1410
51 52 179.8 37543852638208.0000 1126743465263104.0000 0.1090
51 53 179.8 37543852638208.0000 1126743465263104.0000 0.1090
51 54 179.6 40935400407040.0000 1139419390148608.0000 0.1529
54 55 179.9 33217490976768.0000 809496242814976.0000 0.1090
54 56 179.9 33217490976768.0000 809496242814976.0000 0.1090
54 57 179.4 28906685988864.0000 670354737463296.0000 0.1410
57 58 178.6 20725337423872.0000 344853258960896.0000 0.1410
58 59 179.0 19086866120704.0000 256434931499008.0000 0.1090
58 60 179.0 19086866120704.0000 256434931499008.0000 0.1090
58 61 178.8 18870247096320.0000 242751148916736.0000 0.1529
61 62 178.8 13515123326976.0000 143391006392320.0000 0.1090
61 63 178.8 13515123326976.0000 143391006392320.0000 0.1090
61 64 178.8 9849360351232.0000 107687001980928.0000 0.1410
64 65 178.7 3544029331456.0000 34019745988608.0000 0.0945
Back Off! I just backed up step866.pdb to ./#step866.pdb.5#
Back Off! I just backed up step867.pdb to ./#step867.pdb.4#
Wrote pdb files with previous and current coordinates
Step 868, time 1.736 (ps) LINCS WARNING
relative constraint deviation after LINCS:
max inf (between atoms 15 and 16) rms inf
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
1 2 178.4 3977670819840.0000 152569821265920.0000 0.1090
1 3 178.4 3977670819840.0000 152569821265920.0000 0.1090
1 4 178.4 3977670819840.0000 152569821265920.0000 0.1090
1 5 178.1 8551896973312.0000 945681938251776.0000 0.1529
5 6 178.1 10609417519104.0000 1047706134904832.0000 0.1090
5 7 178.1 10609417519104.0000 1047706134904832.0000 0.1090
5 8 177.5 13921285046272.0000 4457932582289408.0000 0.1410
8 9 177.9 26209574453248.0000 42241372723347456.0000 0.1410
9 10 178.3 31550504697856.0000 46386660409081856.0000 0.1090
9 11 178.3 31550508892160.0000 46386660409081856.0000 0.1090
9 12 177.1 43108314120192.0000 413868786718867456.0000 0.1529
12 13 178.2 41816460099584.0000 439770188292816896.0000 0.1090
12 14 178.2 41816455905280.0000 439770188292816896.0000 0.1090
12 15 176.8 47497573564416.0000 2374783212908969984.0000 0.1410
15 16 177.8 73381714067456.0000 22764869283613769728.0000 0.1410
16 17 178.3 85125429723136.0000 25092735510731816960.0000 0.1090
16 18 178.3 85125421334528.0000 25092735510731816960.0000 0.1090
16 19 176.5 119592206729216.0000 179852077951784845312.0000 0.1529
19 20 177.4 115651775561728.0000 193812585885749739520.0000 0.1090
19 21 177.4 115651775561728.0000 193812585885749739520.0000 0.1090
19 22 175.9 139935948472320.0000 700273994734069874688.0000 0.1410
22 23 177.6 242612669775872.0000 3288624712347971223552.0000 0.1410
23 24 178.5 286189374406656.0000 3917898614531615096832.0000 0.1090
23 25 178.5 286189374406656.0000 3917898614531615096832.0000 0.1090
23 26 177.3 421234454036480.0000 12050427889943125688320.0000 0.1529
26 27 178.4 418777766297600.0000 13255632808524023595008.0000 0.1090
26 28 178.4 418777766297600.0000 13255632808524023595008.0000 0.1090
26 29 177.4 511880510570496.0000 28815834107567195291648.0000 0.1410
29 30 179.0 875089654448128.0000 87537186533140710031360.0000 0.1410
30 31 179.6 1039885737656320.0000 107987239807495715160064.0000 0.1090
30 32 179.6 1039885737656320.0000 107987239807495715160064.0000 0.1090
30 33 179.5 1405206327721984.0000 188008386936916313899008.0000 0.1529
33 34 179.8 1360967627702272.0000 200886826388149455814656.0000 0.1090
33 35 179.8 1360967627702272.0000 200886826388149455814656.0000 0.1090
33 36 179.5 1475370658299904.0000 261184711151080100069376.0000 0.1410
36 37 179.9 2011543101243392.0000 461002905405248575111168.0000 0.1410
37 38 179.8 2307230393171968.0000 558625236771140660101120.0000 0.1090
37 39 179.8 2307230393171968.0000 558625236771140660101120.0000 0.1090
37 40 180.0 2763734682435584.0000 678782535837281157120000.0000 0.1529
40 41 179.9 2500746318708736.0000 631513474724340810383360.0000 0.1090
40 42 179.9 2500746318708736.0000 631513474724340810383360.0000 0.1090
40 43 180.0 2357986169192448.0000 586434099779025017765888.0000 0.1410
43 44 179.9 2302985086435328.0000 550810374524945261658112.0000 0.1410
44 45 179.9 2404420939677696.0000 566234806931922001854464.0000 0.1090
44 46 179.9 2404420939677696.0000 566234806931922001854464.0000 0.1090
44 47 179.9 2621617704271872.0000 595544053162864095002624.0000 0.1529
47 48 179.8 2153688130912256.0000 471244054929092064051200.0000 0.1090
47 49 179.8 2153688130912256.0000 471244018900295045087232.0000 0.1090
47 50 179.8 1850107494400000.0000 386140793778567464878080.0000 0.1410
50 51 179.2 1267195740946432.0000 204118519408757976334336.0000 0.1410
51 52 179.6 1126743465263104.0000 149197860543313666375680.0000 0.1090
51 53 179.6 1126743465263104.0000 149197860543313666375680.0000 0.1090
51 54 179.1 1139419390148608.0000 137907426349488380313600.0000 0.1529
54 55 179.3 809496242814976.0000 74584167472078312701952.0000 0.1090
54 56 179.3 809496242814976.0000 74584167472078312701952.0000 0.1090
54 57 178.8 670354737463296.0000 60551036601584767205376.0000 0.1410
57 58 177.5 344853258960896.0000 18237673468208131080192.0000 0.1410
58 59 178.0 256434931499008.0000 7318891515282200723456.0000 0.1090
58 60 178.0 256434931499008.0000 7318891515282200723456.0000 0.1090
58 61 177.5 242751148916736.0000 6663794535785167847424.0000 0.1529
61 62 178.5 143391006392320.0000 1703730175645233184768.0000 0.1090
61 63 178.5 143391006392320.0000 1703730175645233184768.0000 0.1090
61 64 178.6 107687001980928.0000 1430247962373252972544.0000 0.1410
64 65 178.8 34019745988608.0000 249595507876500078592.0000 0.0945
Back Off! I just backed up step867.pdb to ./#step867.pdb.5#
Back Off! I just backed up step868.pdb to ./#step868.pdb.2#
Wrote pdb files with previous and current coordinates
-------------------------------------------------------
Program mdrun, VERSION 3.3
Source code file: nsgrid.c, line: 226
Range checking error:
Explanation: During neighborsearching, we assign each particle to a grid
based on its coordinates. If your system contains collisions or parameter
errors that give particles very high velocities you might ehe nd up with some
coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
put these on a grid, so this is usually where we detect those errors.
Make sure your system is properly energy-minimized and that the potential
energy seems reasonable before trying again.
Variable ci has value -2147483648. It should have been within [ 0 .. 10648 ]
Please report this to the mailing list (gmx-users at gromacs.org)
-------------------------------------------------------
"
then i added the [ pairs ] for
in page 91 mannual 3.2 there is a sentence
"The GROMACS and GROMOS force fields lists all these interactions explicitly, but this section might be empty for force fields like OPLS that calculate the 1-4 interactions by scaling."
this means the [ pairs ] can be listed in OPLS
and my simulation went perfectly well
then is it necessary to delete those [ pairs ] in OPLS as stated in mannual3.2 page 103 ???
i've simulated systems that went well with or without [ pairs ] listed using OPLS, BUT the results didn't seem to have much difference!
Regards
Thanks
Rongliang Wu
wurl04 at iccas.ac.cn
2006-04-05
More information about the gromacs.org_gmx-users
mailing list