* Vitaly Chaban <[email protected]> [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: [email protected],[email protected] skype: vvchaban, mob.: +38-097-8259698 _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting!Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected].Can't post? Read http://www.gromacs.org/mailing_lists/users.php
-- Florian Dommert Dipl.-Phys. Institute for Computational Physics University Stuttgart Pfaffenwaldring 27 70569 Stuttgart EMail: [email protected] Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert
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