[gmx-users] destruction of the structure of a molecule in water after energy minimization
Justin Lemkul
jalemkul at vt.edu
Fri Jun 2 12:42:54 CEST 2017
On 6/2/17 4:26 AM, Saeed Nasiri wrote:
>>
>> Dear *Justin*
>>
>> I checked all of the parameters again and again and I try that to prepare
>> them similar to the opls itp files.
>> However, the problem does not solve. Also, when the energy minimization
>> has been run there is warning about 1-4 interaction. I think
>> that the problem is related to this warning.
>>
It is, and like I said before, this is either coming from the topology or bad
coordinates. Read
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
If a single molecule of BMI distorts in vacuo, you have a fundamental problem in
whatever you're trying to do.
-Justin
>> Thank you so much in advanced for your help.
>>
>>
>> " ....
>> Step= 44, Dmax= 3.2e-01 nm, Epot= 1.06264e+09 Fmax= 1.09629e+10, atom=
>> 13
>> WARNING: Listed nonbonded interaction between particles 11 and 14
>> at distance 2.004 which is larger than the table limit 2.000 nm.
>>
>> This is likely either a 1,4 interaction, or a listed interaction inside
>> a smaller molecule you are decoupling during a free energy calculation.
>> Since interactions at distances beyond the table cannot be computed,
>> they are skipped until they are inside the table limit again. You will
>> only see this message once, even if it occurs for several interactions.
>>
>> IMPORTANT: This should not happen in a stable simulation, so there is
>> probably something wrong with your system. Only change the table-extension
>> distance in the mdp file if you are really sure that is the reason.
>> ... "
>>
>>
>> ########## topol.top ################
>> #include "oplsaa.ff/forcefield.itp"
>>
>>
>> #include "ff_BMI.itp"
>> #include "BMI.itp"
>> #include "Cl.itp"
>>
>> ; Include water topology
>> #include "oplsaa.ff/tip3p.itp"
>>
>> [system]
>> BMI Cl
>>
>> [molecules]
>> BMI 1
>> Cl 1
>>
>> ######### BMI.itp #################
>> [ moleculetype ]
>> ; Name nrexcl
>> BMI 3
>>
>> [ atoms ]
>> ; nr type resnr residue atom cgnr charge mass
>> 1 CW 1 BMI CW 1 -0.13 12.011
>> 2 CW 1 BMI CW 2 -0.13 12.011
>> 3 CR 1 BMI CR 3 -0.11 12.011
>> 4 HCW 1 BMI HCW 4 0.21 1.008
>> 5 HCW 1 BMI HCW 5 0.21 1.008
>> 6 HCR 1 BMI HCR 6 0.21 1.008
>> 7 NA 1 BMI NA 7 0.15 14.007
>> 8 NA 1 BMI NA 8 0.15 14.007
>> 9 C1 1 BMI C1 9 -0.17 12.011
>> 10 H1 1 BMI H1 10 0.13 1.008
>> 11 H1 1 BMI H1 11 0.13 1.008
>> 12 C2 1 BMI C2 12 0.01 12.011
>> 13 HC 1 BMI HC 13 0.06 1.008
>> 14 HC 1 BMI HC 14 0.06 1.008
>> 15 CS 1 BMI CS 15 -0.12 12.011
>> 16 HC 1 BMI HC 16 0.06 1.008
>> 17 HC 1 BMI HC 17 0.06 1.008
>> 18 CT 1 BMI CT 18 -0.18 12.011
>> 19 HC 1 BMI HC 19 0.06 1.008
>> 20 HC 1 BMI HC 20 0.06 1.008
>> 21 HC 1 BMI HC 21 0.06 1.008
>> 22 C1 1 BMI C1 22 -0.17 12.011
>> 23 H1 1 BMI H1 23 0.13 1.008
>> 24 H1 1 BMI H1 24 0.13 1.008
>> 25 H1 1 BMI H1 25 0.13 1.008
>>
>>
>> [ bonds ]
>> ; ai aj funct
>> 1 2 6
>> 1 4 6
>> 1 7 6
>>
>> 2 5 6
>> 2 8 6
>>
>> 3 6 6
>> 3 7 6
>> 3 8 6
>>
>> 7 22 6
>>
>> 8 9 6
>>
>> 9 10 6
>> 9 11 6
>> 9 12 6
>>
>> 12 13 6
>> 12 14 6
>> 12 15 6
>>
>> 15 16 6
>> 15 17 6
>> 15 18 6
>>
>> 18 19 6
>> 18 20 6
>> 18 21 6
>>
>> 22 23 6
>> 22 24 6
>> 22 25 6
>>
>> [ pairs ]
>> ; ai aj funct c0 c1 c2 c3
>>
>> 1 8 1
>> 1 6 1
>> 1 23 1
>> 1 24 1
>> 1 25 1
>> 1 9 1
>>
>> 2 6 1
>> 2 7 1
>> 2 10 1
>> 2 11 1
>> 2 12 1
>> 2 22 1
>>
>> 3 1 1
>> 3 5 1
>> 3 4 1
>> 3 23 1
>> 3 24 1
>> 3 25 1
>> 3 10 1
>> 3 11 1
>> 3 12 1
>>
>> 4 22 1
>> 4 5 1
>> 4 8 1
>>
>> 5 7 1
>> 5 9 1
>>
>> 6 22 1
>> 6 9 1
>>
>> 7 8 1
>> 7 9 1
>>
>> 8 22 1
>> 8 13 1
>> 8 14 1
>> 8 15 1
>>
>> 9 16 1
>> 9 17 1
>> 9 18 1
>>
>> 10 13 1
>> 10 14 1
>> 10 15 1
>>
>> 11 13 1
>> 11 14 1
>> 11 15 1
>>
>> 12 19 1
>> 12 20 1
>> 12 21 1
>>
>> 13 16 1
>> 13 17 1
>> 13 18 1
>>
>> 14 16 1
>> 14 17 1
>> 14 18 1
>>
>> 16 19 1
>> 16 20 1
>> 16 21 1
>>
>> 17 19 1
>> 17 20 1
>> 17 21 1
>>
>> [ angles ]
>> ; ai aj ak funct
>>
>> 1 7 22 1
>> 1 7 3 1
>> 1 2 5 1
>> 1 2 8 1
>>
>> 2 1 4 1
>> 2 1 7 1
>> 2 8 3 1
>> 2 8 9 1
>>
>> 3 7 22 1
>> 3 8 9 1
>>
>> 4 1 7 1
>>
>> 5 2 8 1
>>
>> 6 3 7 1
>> 6 3 8 1
>>
>> 7 22 23 1
>> 7 22 24 1
>> 7 22 25 1
>> 7 3 8 1
>>
>> 8 9 10 1
>> 8 9 11 1
>> 8 9 12 1
>>
>> 9 12 13 1
>> 9 12 14 1
>> 9 12 15 1
>>
>> 10 9 11 1
>> 10 9 12 1
>>
>> 11 9 12 1
>>
>> 12 15 16 1
>> 12 15 17 1
>> 12 15 18 1
>>
>> 13 12 14 1
>> 13 12 15 1
>>
>> 14 12 15 1
>>
>> 15 18 19 1
>> 15 18 20 1
>> 15 18 21 1
>>
>> 16 15 17 1
>> 16 15 18 1
>>
>> 17 15 18 1
>>
>> 19 18 20 1
>> 19 18 21 1
>>
>> 20 18 21 1
>>
>> 23 22 24 1
>> 23 22 25 1
>>
>> 24 22 25 1
>>
>>
>> [ dihedrals ]
>>
>> ; ai aj ak al funct
>>
>> 1 2 8 3 5
>> 1 2 8 9 5
>> 1 7 3 6 5
>> 1 7 22 23 5
>> 1 7 22 24 5
>> 1 7 22 25 5
>> 1 7 3 6 5
>> 1 7 3 8 5
>>
>> 2 1 7 22 5
>> 2 1 7 3 5
>> 2 8 3 6 5
>> 2 8 3 7 5
>> 2 8 9 10 5
>> 2 8 9 11 5
>> 2 8 9 12 5
>>
>> 3 7 1 4 5
>> 3 7 22 23 5
>> 3 7 22 24 5
>> 3 7 22 25 5
>> 3 8 2 5 5
>> 3 8 9 10 5
>> 3 8 9 11 5
>> 3 8 9 12 5
>>
>> 4 1 2 5 5
>> 4 1 2 8 5
>> 4 1 7 22 5
>>
>> 5 2 1 7 5
>> 5 2 8 9 5
>>
>> 6 3 7 22 5
>> 6 3 8 9 5
>>
>> 7 3 8 9 5
>> 7 1 2 8 5
>>
>> 8 3 7 22 5
>> 8 9 12 13 5
>> 8 9 12 14 5
>> 8 9 12 15 5
>>
>> 9 12 15 16 5
>> 9 12 15 17 5
>> 9 12 15 18 5
>>
>> 10 9 12 13 5
>> 10 9 12 14 5
>> 10 9 12 15 5
>>
>> 11 9 12 13 5
>> 11 9 12 14 5
>> 11 9 12 15 5
>>
>> 12 15 18 19 5
>> 12 15 18 20 5
>> 12 15 18 21 5
>>
>> 13 12 15 16 5
>> 13 12 15 17 5
>> 13 12 15 18 5
>>
>> 14 12 15 16 5
>> 14 12 15 17 5
>> 14 12 15 18 5
>>
>> 16 15 18 19 5
>> 16 15 18 20 5
>> 16 15 18 21 5
>>
>> 17 15 18 19 5
>> 17 15 18 20 5
>> 17 15 18 21 5
>>
>>
>> [ dihedrals ]
>> ; ai aj ak al funct c0 c1
>> c2 c3
>>
>> 3 1 7 22 5 improper_CR_CW_NA_C1
>> 3 8 2 9 5 improper_CR_CW_NA_C1
>>
>> 7 8 3 5 5 improper_NA_NA_CR_HCR
>>
>> 7 1 2 4 5 improper_NA_CW_CW_HCW
>> 8 2 1 5 5 improper_NA_CW_CW_HCW
>>
>>
>> ######## ff_BMI.itp ###############
>>
>> [ defaults ]
>> ; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
>> ;1 3 yes 0.5 0.5
>>
>> [ atomtypes ]
>> ; name bond_type mass charge ptype sigma epsilon
>>
>> C1 6 12.0110 -0.170 A 3.500 0.27614
>> C2 6 12.0110 0.010 A 3.500 0.27614
>> CE 6 12.0110 -0.050 A 3.500 0.27614
>> CS 6 12.0110 -0.120 A 3.500 0.27614
>> CT 6 12.0110 -0.180 A 3.500 0.27614
>> CR 6 12.0110 -0.110 A 3.550 0.29288
>> CW 6 12.0110 -0.130 A 3.550 0.29288
>> HA 1 1.0080 0.210 A 2.420 0.12552
>> HCR 1 1.0080 0.210 A 2.420 0.12552
>> HCW 1 1.0080 0.210 A 2.420 0.12552
>> HC 1 1.0080 0.060 A 2.500 0.12552
>> H1 1 1.0080 0.130 A 2.500 0.12552
>> NA 7 14.0070 0.150 A 3.250 0.71128
>> Cl 1 35.4530 -1.000 A 3.650 0.83000
>>
>>
>> [ bondtypes ]
>>
>> ; i j func b0(re/nm) kb (kj/molnm^2)
>>
>>
>> HC CT 6 0.1090 -284500
>> HC CS 6 0.1090 -284500
>> HC C2 6 0.1090 -284500
>> HC C1 6 0.1090 -284500
>> H1 C1 6 0.1090 -284500
>>
>> CT CS 6 0.1529 224200
>> CS C2 6 0.1529 224200
>> C2 C1 6 0.1529 224200
>>
>> CR HCR 6 0.1080 -284500
>> CW HCW 6 0.1080 -284500
>> CR NA 6 0.1315 399200
>> CW NA 6 0.1378 357400
>> CW CW 6 0.1341 435200
>> NA C1 6 0.1466 141000
>>
>>
>> [ angletypes ]
>> ; i j k type th/deg ka/kjmol-1
>>
>>
>> CT CS C2 1 112.700 488.300
>> CS C2 C1 1 112.700 488.300
>> C2 C1 NA 1 112.700 488.300
>>
>> CS CT HC 1 110.700 313.800
>> CT CS HC 1 110.700 313.800
>> C2 CS HC 1 110.700 313.800
>> C2 C1 H1 1 110.700 313.800
>> C1 C2 HC 1 110.700 313.800
>> CS C2 HC 1 110.700 313.800
>>
>> HC CT HC 1 107.800 276.100
>> HC CS HC 1 107.800 276.100
>> HC C2 HC 1 107.800 276.100
>> H1 C1 H1 1 107.800 276.100
>>
>>
>> CW NA CR 1 108.000 585.800
>> CW NA C1 1 125.600 585.800
>> CR NA C1 1 126.400 585.800
>> NA CR HCR 1 125.100 292.900
>> NA CR NA 1 109.800 585.800
>> NA CW CW 1 107.100 585.800
>> NA CW HCW 1 122.000 292.900
>> CW CW HCW 1 130.900 292.900
>> NA C1 H1 1 110.700 313.800
>> NA C1 C2 1 112.700 488.300
>>
>> [ dihedraltypes ]
>> ; i j k l type v1 v2 v3 v4
>>
>> HC CT CS HC 5 0.00000 0.00000 1.33050
>> 0.00000
>> HC CS C2 HC 5 0.00000 0.00000 1.33050
>> 0.00000
>> HC C2 C1 H1 5 0.00000 0.00000 1.33050
>> 0.00000
>>
>> CT CS C2 HC 5 0.00000 0.00000 1.53130
>> 0.00000
>> CS C2 C1 H1 5 0.00000 0.00000 1.53130
>> 0.00000
>> C1 C2 CS HC 5 0.00000 0.00000 1.53130
>> 0.00000
>> C2 CS CT HC 5 0.00000 0.00000 1.53130
>> 0.00000
>> CT CS C2 C1 5 7.28000 -0.65690 1.16730
>> 0.00000
>>
>> CW NA CR NA 5 0.00000 19.46000 0.00000
>> 0.00000
>> CW NA CR HCR 5 0.00000 19.46000 0.00000
>> 0.00000
>> C1 NA CR NA 5 0.00000 19.46000 0.00000
>> 0.00000
>> C1 NA CR HCR 5 0.00000 19.46000 0.00000
>> 0.00000
>> CR NA CW CW 5 0.00000 12.55000 0.00000
>> 0.00000
>> CR NA CW HCW 5 0.00000 12.55000 0.00000
>> 0.00000
>> C1 NA CW CW 5 0.00000 12.55000 0.00000
>> 0.00000
>> C1 NA CW HCW 5 0.00000 12.55000 0.00000
>> 0.00000
>> NA CW CW NA 5 0.00000 44.98000 0.00000
>> 0.00000
>> NA CW CW HCW 5 0.00000 44.98000 0.00000
>> 0.00000
>> HCW CW CW HCW 5 0.00000 44.98000 0.00000
>> 0.00000
>> CW NA C1 H1 5 0.00000 0.00000 0.51900
>> 0.00000
>> CR NA C1 H1 5 0.00000 0.00000 0.00000
>> 0.00000
>> CW NA C1 C2 5 -7.15350 6.10640 0.79390
>> 0.00000
>> CR NA C1 C2 5 -5.26910 0.00000 0.00000
>> 0.00000
>> NA C1 C2 CS 5 -7.47970 3.16420 -1.20260
>> 0.00000
>> NA C1 C2 HC 5 0.00000 0.00000 0.36700
>> 0.00000
>>
>> [ dihedraltypes ]
>>
>>
>> #define improper_CR_CW_NA_C1 0.00000 8.37000 0.00000 0.00000
>> #define improper_NA_NA_CR_HCR 0.00000 9.20000 0.00000 0.00000
>> #define improper_NA_CW_CW_HCW 0.00000 9.20000 0.00000 0.00000
>>
>> ###########################################################
>>
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
==================================================
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