[gmx-users] g_velacc -mol option

[Vigneshwar Ramakrishnan]

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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