[gmx-users] Ask about improper angle energy

[alexander yakovenko]

Dear gromacs developers, 
 
I have the structure of formaldehyde molecule: 
 
REMARK    GENERATED BY TRJCONV 
HEADER    Protein t=   0.00100 
REMARK    THIS IS A SIMULATION BOX 
CRYST1   61.800   61.890   60.000  90.00  90.00  90.00 P 1           1 
MODEL        2 
ATOM      1  C   LIG     1      30.920  30.938  30.001  1.00  0.00 
ATOM      2  O   LIG     1      29.689  30.943  30.000  1.00  0.00 
ATOM      3  H   LIG     1      31.487  31.880  29.996  1.00  0.00 
ATOM      4  H00 LIG     1      31.505  29.989  29.985  1.00  0.00 
TER 
ENDMDL 
 
and energy of improper angle from energy.xvg: 
    0.001000    0.043663 
 
The rtp string is: 
  C      O     H     H00        0.000000    564.359985 
 
  But the calculated improper is: 
  1.328Deg->0.0232Rad 
  The formula of improper energy from GROMACS manual is: 
  E=k*(value-optimal_value)^2 
 
  and E=564.36*(0.0232)^2=0.3029 
that is  substantialy higher than extracted from trajectory. 
Would you please to help me to find mistake in my calculations? 
 
Thank you, 
Best regards, 
 
Alexander Yakovenko 
Institute of Molecular Biology & Genetic of NAS of Ukraine 
03143 
acad.Zabolotnogo str. 150 
Kiev 
Ukraine 
______________________________________________ 
E-mail: yakovenko_a at ukr.net