Dear Users, I am trying the calculate the velocity autocorrelation function of molecules. g_velacc has the -mol option.
I would like to know/confirm how the velocity autocorrelation function of *molecules* is calculated. Is it calculated from the center of mass velocity of each of the molecules? I calculated the VAC of 1 molecule using the g_velacc -mol option and compared it with a separate calculation wherein 1. I wrote down the center of mass velocity of the molecule in each direction, (g_traj -com option) 2. calculated the ACF in each direction (g_analyze -ac option) 3. and added the ACF of each component. The values gromacs gives and the values I calculate are almost identical (with a difference of ~0.0004). I would like to confirm if my understanding of the calculation of VAC of Molecule is correct. (That is, the VAC is calculated for the center of mass velocity when -mol option is specified.) Secondly, as per the manual, I am supposed to give the molecule number in the index file for g_velacc -mol option. However, gromacs gives an error if I do so, printing: * Fatal error: The index group does not consist of whole molecules For more information and tips for troubleshooting, please check the GROMACS* My index file was: [r25] 25 Is this a bug, or am I missing something? Thanks very much, Vignesh -- R.Vigneshwar Graduate Student, Dept. of Chemical & Biomolecular Engg, National University of Singapore, Singapore "Strive for Excellence, Never be satisfied with the second Best!!" I arise in the morning torn between a desire to improve the world and a desire to enjoy the world. This makes it hard to plan the day. (E.B. White)
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