[gmx-users] g_vellac in the last versions

[Vitaly Chaban]

Hi,

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
initially...

Trying
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
g_msd).

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

Thanks,
Vitaly

-- 
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