Hi Mark
My Apologies. Here is more info.
gmxdump -f traj.trr >history
>From history I take the coordinates at 250 ps and convert to gro file
say test.gro
trjconv -f traj.trr -dump 250 -o frame5.gro
I then compare frame5.gro with test.gro
Please find attached an excerpts of both files (in one file) and pay
attention to the sign difference of the x coordinate at atom s 38 50 51 59
Cheers
Gavin
Mark Abraham wrote:
> On 2/11/2011 10:23 PM, Gavin Melaugh wrote:
>> Hi all
>>
>> I have generated a gro file from a traj.trr file using trjconv. When I
>> use gmxdump on the same traj.trr file to output a generic format history
>> file it seems that there is a discrepancy in the coordinates of some
>> atoms in a particular frame. Essentially I output frame 5 using trjconv,
>> then I take the corresponding frame from the history file and covert it
>> to gro format. I then run vimdiff on the two files. There are sign
>> differences with the coordiante components. The atoms in question are at
>> the edge of the periodic box. I was just wondering why there is a
>> discrepancy in the two utilities?
>
> Without actual command lines that produced output and actual examples
> of what you think is anomalous we can't say.
>
> Mark
History trajdump
240 240
1CGE CA 1 0.287 4.485 6.345 1CGE CA 1
0.287 4.485 6.345
1CGE CB 2 0.381 4.539 6.442 1CGE CB 2
0.381 4.539 6.442
1CGE HC 3 0.182 4.477 6.373 1CGE HC 3
0.182 4.477 6.373
1CGE CA 4 0.504 4.564 6.391 1CGE CA 4
0.504 4.564 6.391
1CGE CB 5 0.551 4.515 6.264 1CGE CB 5
0.551 4.515 6.264
1CGE HC 6 0.570 4.621 6.446 1CGE HC 6
0.570 4.621 6.446
1CGE CA 7 0.467 4.440 6.181 1CGE CA 7
0.467 4.440 6.181
1CGE CB 8 0.328 4.437 6.218 1CGE CB 8
0.328 4.437 6.218
1CGE HC 9 0.506 4.388 6.096 1CGE HC 9
0.506 4.388 6.096
1CGE CU 10 0.336 4.595 6.579 1CGE CU 10
0.336 4.595 6.579
1CGE NU 11 0.232 4.544 6.631 1CGE NU 11
0.232 4.544 6.631
1CGE CH 12 0.161 4.574 6.757 1CGE CH 12
0.161 4.574 6.757
1CGE CU 13 0.692 4.527 6.217 1CGE CU 13
0.692 4.527 6.217
1CGE NU 14 0.754 4.485 6.119 1CGE NU 14
0.754 4.485 6.119
1CGE CH 15 0.897 4.530 6.127 1CGE CH 15
0.897 4.530 6.127
1CGE CU 16 0.231 4.395 6.122 1CGE CU 16
0.231 4.395 6.122
1CGE NU 17 0.107 4.398 6.158 1CGE NU 17
0.107 4.398 6.158
1CGE CH 18 0.002 4.359 6.070 1CGE CH 18
0.002 4.359 6.070
1CGE CA 19 0.633 5.058 5.960 1CGE CA 19
0.633 5.058 5.960
1CGE CB 20 0.690 4.968 6.057 1CGE CB 20
0.690 4.968 6.057
1CGE HC 21 0.662 5.025 5.854 1CGE HC 21
0.662 5.025 5.854
1CGE CA 22 0.677 4.992 6.193 1CGE CA 22
0.677 4.992 6.193
1CGE CB 23 0.577 5.090 6.231 1CGE CB 23
0.577 5.090 6.231
1CGE HC 24 0.714 4.916 6.260 1CGE HC 24
0.714 4.916 6.260
1CGE CA 25 0.509 5.175 6.140 1CGE CA 25
0.509 5.175 6.140
1CGE CB 26 0.536 5.158 5.996 1CGE CB 26
0.536 5.158 5.996
1CGE HC 27 0.434 5.238 6.178 1CGE HC 27
0.434 5.238 6.178
1CGE CU 28 0.773 4.848 6.011 1CGE CU 28
0.773 4.848 6.011
1CGE NU 29 0.847 4.767 6.083 1CGE NU 29
0.847 4.767 6.083
1CGE CH 30 0.922 4.651 6.042 1CGE CH 30
0.922 4.651 6.041
1CGE CU 31 0.555 5.129 6.374 1CGE CU 31
0.555 5.129 6.374
1CGE NU 32 0.626 5.070 6.467 1CGE NU 32
0.626 5.070 6.467
1CGE CH 33 0.609 5.112 6.607 1CGE CH 33
0.609 5.112 6.607
1CGE CU 34 0.466 5.249 5.900 1CGE CU 34
0.466 5.249 5.900
1CGE NU 35 0.501 5.268 5.786 1CGE NU 35
0.501 5.268 5.786
1CGE CH 36 0.430 5.358 5.698 1CGE CH 36
0.430 5.358 5.698
1CGE CA 37 0.030 5.088 5.902 1CGE CA 37
0.030 5.088 5.902
1CGE CB 38 0.043 5.009 5.996 1CGE CB 38
-0.043 5.009 5.996
1CGE HC 39 0.022 5.199 5.907 1CGE HC 39
0.022 5.199 5.907
1CGE CA 40 7.353 4.868 5.988 1CGE CA 40
7.353 4.868 5.988
1CGE CB 41 7.435 4.804 5.897 1CGE CB 41
7.435 4.804 5.897
1CGE HC 42 7.310 4.801 6.073 1CGE HC 42
7.310 4.801 6.073
1CGE CA 43 0.131 4.879 5.819 1CGE CA 43
0.131 4.879 5.819
1CGE CB 44 0.123 5.022 5.826 1CGE CB 44
0.123 5.022 5.826
1CGE HC 45 0.180 4.834 5.732 1CGE HC 45
0.180 4.834 5.732
1CGE CU 46 7.255 5.072 6.092 1CGE CU 46
7.255 5.072 6.092
1CGE NU 47 7.245 5.186 6.105 1CGE NU 47
7.245 5.186 6.105
1CGE CH 48 7.174 5.260 6.193 1CGE CH 48
7.174 5.260 6.193
1CGE CU 49 0.047 4.656 5.894 1CGE CU 49
0.047 4.656 5.894
1CGE NU 50 0.016 4.578 5.966 1CGE NU 50
-0.016 4.578 5.966
1CGE CH 51 0.002 4.439 5.938 1CGE CH 51
-0.002 4.439 5.938
1CGE CU 52 0.222 5.103 5.730 1CGE CU 52
0.222 5.103 5.730
1CGE NU 53 0.224 5.230 5.713 1CGE NU 53
0.224 5.230 5.713
1CGE CH 54 0.309 5.292 5.621 1CGE CH 54
0.309 5.292 5.621
1CGE CA 55 0.116 5.073 6.528 1CGE CA 55
0.116 5.073 6.528
1CGE CB 56 0.190 5.014 6.627 1CGE CB 56
0.190 5.014 6.627
1CGE HC 57 0.169 5.140 6.457 1CGE HC 57
0.169 5.140 6.457
1CGE CA 58 0.134 4.920 6.721 1CGE CA 58
0.134 4.920 6.721
1CGE CB 59 0.009 4.901 6.719 1CGE CB 59
-0.009 4.901 6.719
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