[gmx-users] grompp Segmentation fault

Nilesh Dhumal ndhumal at andrew.cmu.edu
Tue Oct 14 14:31:54 CEST 2014


Here are more details
.itp file

; Derived from parsing of runfiles/alat.top.orig
[ defaults ]
; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
 1               3               yes             0.5     0.5
; comb-rule 3 is square-root sigma, the OPLSAA version

[ atomtypes ]
; full atom descriptions are available in ffoplsaa.atp
; name  bond_type    mass    charge   ptype          sigma      epsilon
 opls_991   Cu    29	63.54600    1.098       A    3.114e-01    0.02092e+00
 opls_993   OA    8     15.99940    -0.665       A    3.033e-01   
0.401664e+00
 opls_994   OB    8     15.99940    -0.665       A    3.033e-01   
0.401664e+00
 opls_995   CA    6     12.0110      0.778       A    3.473e-01   
0.39748e+00
 opls_996   CB    6     12.0110     -0.092       A    3.473e-01   
0.39748e+00
 opls_997   CC    6     12.0110     -0.014       A    3.473e-01   
0.39748e+00
 opls_998   HM    1      1.0080      0.109       A    2.846e-01   
0.06276e+00

[ bondtypes ]
; i    j  func       b0        D          Beta
 Cu   OA   3     0.1969     358.857496    0.285
 Cu   OB   3     0.1969     358.857496    0.285
 OA   CA   3     0.1260     564.84        0.200
 OB   CA   3     0.1260     564.84        0.200
 CA   CB   3     0.1456     367.52256     0.200
 CB   CC   3     0.1355     502.08        0.200
 CC   HM   3     0.0931     485.344       0.177

 [ angletypes ]
;  i    j    k  func       th0       cth
OA   Cu   OA      1       170.2       419.73888
OB   Cu   OB      1       170.2       419.73888
OA   Cu   OB      1        90.0       100.416
Cu   OA   CA      1       127.5       338.65296
Cu   OB   CA      1       127.5       338.65296
OA   CA   OA      1       128.5       606.68
OB   CA   OB      1       128.5       606.68
OA   CA   OB      1       128.5       606.68
OA   CA   CB      1       116.2       456.01416
OB   CA   CB      1       116.2       456.01416
CA   CB   CC      1       119.9       290.20224
CC   CB   CC      1       120.1       753.12
CB   CC   CB      1       119.9       753.12
CB   CC   HM      1       120.0       309.616

[ dihedraltypes ]
;  i    j    k    l   func     coefficients
; OPLS Fourier dihedraltypes translated to Gromacs Ryckaert-Bellemans form
; according to the formula in the Gromacs manual.
Cu    OA   CA   CB    1     180.0    12.552     2
Cu    OB   CA   CB    1     180.0    12.552     2
Cu    OA   CA   OB    1     180.0    12.552     2
Cu    OB   CA   OA    1     180.0    12.552     2
Cu    OA   CA   OA    1     180.0    12.552     2
Cu    OB   CA   OB    1     180.0    12.552     2
CB    CC   CB   CC    1     180.0    12.552     2
CA    CB   CC   CB    1     180.0    12.552     2
CA    CB   CC   HM    1     180.0    12.552     2
CC    CB   CC   HM    1     180.0    12.552     2
OA    CA   CB   CC    1     180.0    10.460     2
OB    CA   CB   CC    1     180.0    10.460     2


HM    CC   CB   CB    2     180.0    1.54808    2
CA    CB   CC   CC    2     180.0   41.84       2
CB    CA   OA   OB    2     180.0   41.84       2
CB    CA   OB   OA    2     180.0   41.84       2


Initial part of .gro file

Title
  156
    1BTC  OA1      1  19.579  14.561  18.006  0.0000  0.0000  0.0000
    1BTC  CA2      2  18.533  15.007  18.533  0.0000  0.0000  0.0000
    1BTC  CB3      3  17.865  16.163  17.865  0.0000  0.0000  0.0000
    1BTC  CC4      4  18.433  16.737  16.737  0.0000  0.0000  0.0000
    1BTC  HM5      5  19.215  16.358  16.358  0.0000  0.0000  0.0000
    1BTC  CC6      6  16.737  16.737  18.433  0.0000  0.0000  0.0000
    1BTC  HM7      7  16.358  16.358  19.215  0.0000  0.0000  0.0000
    1BTC  OA8      8  14.561  18.006  19.579  0.0000  0.0000  0.0000
    1BTC  CA9      9  15.007  18.533  18.533  0.0000  0.0000  0.0000
    1BTC  CB10    10  16.163  17.865  17.865  0.0000  0.0000  0.0000
    1BTC  CC11    11  16.737  18.433  16.737  0.0000  0.0000  0.0000
    1BTC  HM12    12  16.358  19.215  16.358  0.0000  0.0000  0.0000
    1BTC  OA13    13  18.006  19.579  14.561  0.0000  0.0000  0.0000
    1BTC  CA14    14  18.533  18.533  15.007  0.0000  0.0000  0.0000
    1BTC  CB15    15  17.865  17.865  16.163  0.0000  0.0000  0.0000
    1BTC  OB16    16  14.561  19.579  18.006  0.0000  0.0000  0.0000
    1BTC  OB17    17  18.006  14.561  19.579  0.0000  0.0000  0.0000
    1BTC  OB18    18  19.579  18.006  14.561  0.0000  0.0000  0.0000
    1BTC  OA19    19  14.561  21.499  19.926  0.0000  0.0000  0.0000
    1BTC  CA20    20  15.007  20.972  20.972  0.0000  0.0000  0.0000
    1BTC  CB21    21  16.163  21.639  21.639  0.0000  0.0000  0.0000
    1BTC  CC22    22  16.737  22.767  21.072  0.0000  0.0000  0.0000
    1BTC  HM23    23  16.358  23.146  20.290  0.0000  0.0000  0.0000
    1BTC  CC24    24  16.737  21.072  22.767  0.0000  0.0000  0.0000
    1BTC  HM25    25  16.358  20.290  23.146  0.0000  0.0000  0.0000
    1BTC  OB26    26  14.561  19.926  21.499  0.0000  0.0000  0.0000
    1BTC  OA27    27  19.926  14.561  21.499  0.0000  0.0000  0.0000
    1BTC  CA28    28  20.972  15.007  20.972  0.0000  0.0000  0.0000
    1BTC  CB29    29  21.639  16.163  21.639  0.0000  0.0000  0.0000
    1BTC  CC30    30  22.768  16.737  21.072  0.0000  0.0000  0.0000





>
> On 10/13/14 10:42 PM, Nilesh Dhumal wrote:
>> hello,
>>
>> I running grompp for simulation. I get Segmentation fault error.
>>
>> grompp -f 600.mdp -c cu.gro -p  cu_btc_1.top -o 1.tpr
>>
>>
>> checking input for internal consistency...
>> processing topology...
>> Segmentation fault
>>
>>
>> Could any one tell what is the problem?
>>
>
> Not without a full debugging back trace.  Seg faults are generic memory
> errors;
> there's nothing at all that can be diagnosed from this message alone.
>
> -Justin
>
> --
> ==================================================
>
> 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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