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: [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
