[gmx-users] Calculation of solvent and solute relaxation times

Erik Marklund erikm at xray.bmc.uu.se
Wed May 9 11:06:23 CEST 2012

I think you should still have COM removal. This compensates for numerical errors coming from the integrator. If you remove the COM of your system the COM of the solute is still allowed to move, it's just that there is not net movement of the entire system.


9 maj 2012 kl. 06.58 skrev Debayan Chakraborty:

> Dear Gromacs users,
>                                  I am trying to find out the solvent relaxation times from my molecular dynamics simulations. I think this might require me to use g_rotacf. But I am not sure how to use this utility to obtain relaxation times for the solvent. Also I would like to like at the center-of-mass velocity autocorrelations and angular velocity autocorrelations for the solute, for this purpose do I need to use comm_mode = no. 
> Thanks,
> Debayan Chakraborty
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Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
phone:    +46 18 471 6688        fax: +46 18 511 755
erikm at xray.bmc.uu.se

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