[gmx-users] g_vellac in the last versions

Florian Dommert dommert at fias.uni-frankfurt.de
Wed Mar 4 23:48:51 CET 2009

* Vitaly Chaban <vvchaban at gmail.com> [2009-02-27 16:50:51 +0200]:

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


  yes there have been changes in the code of g_velacc, to allow
  calculating the diffusion coefficient of molecules and not just the
  momentum autocorrelation function ( we talked about this already, do
  you remember ? )

> 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

This is a wrong description and has to be changed, because the you have
to supply an atom index and from the topology file the molecules are

>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

This sounds strange, because only some parts of the code were changed to
deal with molecules, but the routine calculating the VACF stayed

>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
>gmx-users mailing list    gmx-users at gromacs.org
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Florian Dommert

Institute for Computational Physics
University Stuttgart

Pfaffenwaldring 27
70569 Stuttgart

EMail: dommert at icp.uni-stuttgart.de
Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
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