[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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