[gmx-users] Question about g_covar with -mwa option

[Yen-Ting Lai]

Hi all,

I perform a Essential Dynamics style analysis by using g_covar and g_anaeig. I tried to get the extreme structures along one eigenvector. I found that if I turn on the "mass weighted analysis" option in g_covar. Then the hydrogen coordinates become "nan". And if I turn off that option, the coordinates appear again. Is it a resonable result?

Here is some lines from the extreme structure with "mass weighted analysis" option on:(Please notice that except the H2,H3 atoms, all other hydrogens have "nan" in the coordinate column.)
#################START######################
HEADER    frame t= 0.000
MODEL        0
ATOM      1  N   VAL     1       1.232  -2.849 -11.279  1.00  0.00
ATOM      2  H1  VAL     1         nan     nan     nan  1.00  0.00
ATOM      3  H2  VAL     1       0.866  -3.002 -11.508  1.00  0.00
ATOM      4  H3  VAL     1       0.863  -2.561 -11.207  1.00  0.00
ATOM      5  CA  VAL     1       2.302  -3.422 -10.577  1.00  0.00
ATOM      6  HA  VAL     1         nan     nan     nan  1.00  0.00
ATOM      7  CB  VAL     1       3.316  -2.463 -10.202  1.00  0.00
ATOM      8  HB  VAL     1         nan     nan     nan  1.00  0.00
ATOM      9  CG1 VAL     1       4.743  -2.446 -11.974  1.00  0.00
ATOM     10 HG11 VAL     1         nan     nan     nan  1.00  0.00
ATOM     11 HG12 VAL     1         nan     nan     nan  1.00  0.00
ATOM     12 HG13 VAL     1         nan     nan     nan  1.00  0.00
ATOM     13  CG2 VAL     1       2.208  -0.557  -9.777  1.00  0.00
ATOM     14 HG21 VAL     1         nan     nan     nan  1.00  0.00
ATOM     15 HG22 VAL     1         nan     nan     nan  1.00  0.00
ATOM     16 HG23 VAL     1         nan     nan     nan  1.00  0.00
ATOM     17  C   VAL     1       1.837  -4.154  -9.375  1.00  0.00
ATOM     18  O   VAL     1       1.003  -3.681  -8.681  1.00  0.00
ATOM     19  N   GLU     2       2.365  -5.303  -9.117  1.00  0.00
ATOM     20  H   GLU     2         nan     nan     nan  1.00  0.00
ATOM     21  CA  GLU     2       2.066  -6.149  -7.981  1.00  0.00
ATOM     22  HA  GLU     2         nan     nan     nan  1.00  0.00
ATOM     23  CB  GLU     2       2.094  -7.592  -8.434  1.00  0.00
ATOM     24  HB2 GLU     2         nan     nan     nan  1.00  0.00
ATOM     25  HB3 GLU     2         nan     nan     nan  1.00  0.00
ATOM     26  CG  GLU     2       1.403  -8.470  -7.860  1.00  0.00
ATOM     27  HG2 GLU     2         nan     nan     nan  1.00  0.00
ATOM     28  HG3 GLU     2         nan     nan     nan  1.00  0.00
ATOM     29  CD  GLU     2       1.325  -9.763  -8.498  1.00  0.00
ATOM     30  OE1 GLU     2       1.091 -10.276  -8.848  1.00  0.00
ATOM     31  OE2 GLU     2       1.498 -10.269  -8.683  1.00  0.00
ATOM     32  C   GLU     2       3.017  -5.899  -6.821  1.00  0.00
ATOM     33  O   GLU     2       4.162  -5.909  -6.983  1.00  0.00
##########END##########################################

Thanks in advance.
Yen
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