Dear Users, <br><br>I am trying the calculate the velocity autocorrelation function of molecules. g_velacc has the -mol option. <br><br>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? <br>
I calculated the VAC of 1 molecule using the g_velacc -mol option and compared it with a separate calculation wherein <br><br>1. I wrote down the center of mass velocity of the molecule in each direction, (g_traj -com option)<br>
2. calculated the ACF in each direction (g_analyze -ac option)<br>3. and added the ACF of each component. <br><br>The values gromacs gives and the values I calculate are almost identical (with a difference of ~0.0004). <br>
<br>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.)<br><br>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: <br>
<i><br>Fatal error:<br>The index group does not consist of whole molecules<br>For more information and tips for troubleshooting, please check the GROMACS</i><br><br>My index file was: <br><br>[r25]<br>25<br><br>Is this a bug, or am I missing something? <br>
<br>Thanks very much, <br>Vignesh<br><br><br>-- <br>R.Vigneshwar<br>Graduate Student,<br>Dept. of Chemical & Biomolecular Engg,<br>National University of Singapore,<br>Singapore<br><br>"Strive for Excellence, Never be satisfied with the second Best!!"<br>
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