[gmx-users] g_vellac in the last versions

[Florian Dommert]

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

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

Hello,

  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
>initially...
>

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
found.

>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).

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

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

Flo


>
>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
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-- 
Florian Dommert
Dipl.-Phys.

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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