Hi Flo, Yes, I remember our talk about this problem about a year ago.
So what should be the correct notation now? I just tried g_velacc_402f -acflen 1001 -nonormalize -n an.ndx or g_velacc_402f -acflen 1001 -nonormalize -n an.ndx -mol and then g_analyze -integrate -f vac.xvg but they give me a value close to 0... Thank you, Vitaly >>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 _______________________________________________ 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
