[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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