[gmx-users] g_vellac in the last versions

Vitaly Chaban vvchaban at gmail.com
Fri Feb 27 15:50:51 CET 2009


Please let me know if the g_velacc programme contains any changes
since gmx-3.3.3?

 I try to calculate the diffusion constant with Green-Kubo equation in
the way used in 3.3.3:
$GMXPATH/g_velacc -acflen 1001 -nonormalize -mol -n an.ndx -o vac1_an.xvg
$GMXPATH/g_analyze -f vac1_an.xvg -integrate  > ksd1_an.xvg
where the index file contains the numbers of the needed molecules (not atoms).

If one makes the same call in 4.0.2 it gives an error:
Fatal error:
Need a topology to determine the molecules

If the topology is given one obtains:
Program g_velacc_402f, VERSION 4.0.2
Source code file: gmx_velacc.c, line: 77
Fatal error:
The index group does not consist of whole molecules

Why "whole molecules"? - The programme asks for the molecules number

g_velacc_402f -acflen 1001 -nonormalize -n an.ndx
it works fine but after integration gives an incorrect value of
0.00836 (very close to zero) while it has to be about 2.5 (with

What have been changed since 3.3.3? And what should the correct call
be to find the VAC?


Vitaly V. Chaban, Ph.D. (ABD)
School of Chemistry
V.N. Karazin Kharkiv National University
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: chaban at univer.kharkov.ua,vvchaban at gmail.com
skype: vvchaban, mob.: +38-097-8259698

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