[gmx-users] question regarding g_energy -aver output in gromacs 4.5.4
Dear gmx_users, I have a question regarding the 4.5.4 version of gromacs, and the g_energy program. In the past I had used g_energy with the -aver option, which would give me partial sums along with my instantaneous energy values at each output step. This allowed me to take the difference between two successive partial sums divided by the my nstenergy value to get the average energy over that output period. Now when I use the -aver option my output contains my instantaneous value, and what is said to be the exact average. I have the feeling that this exact average is what I used to calculate by hand, i.e the average of the energy over each output period. I tried to test this by calculating the average by hand using gmxdump and my ener.edr file and my numbers match up to the fourth decimal place, but aren't exactly the same. Is this difference simply because gmxdump is truncating the energy values and giving them to me at lower precision? Am I correct on my assumption of what this -aver option is giving me? Any guidance would be appreciated as I'm not so good at understanding the source code. Thank you in advance Jake Spooner -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Questionable van der waals volumes from g_sas
Hello gmx-users I have been attempting to obtain van der Waal's volumes using the g_sas utility. The command I use to do so is something like g_sas -f hexane.gro -s topol.tpr -probe 0 -tv V_vdw.xvg This seems to give reasonable results for most of my test systems, however when I run the command on an optimized structure of cyclohexane I get a larger van der Waal's volume than that of n-hexane. I think this has to do with the fact that the surface calculation method used in g_sas is missing the void in the centre of the ring. In order to test this I increased the size of the ring, calculating the volumes of icosane and cycloicosane. I found that in this case the volume of the cyclic molecule was expectedly smaller. I tried increasing the number of dots used to draw the dot-surface but saw no significant change in the volumes. Therefore my question is if anybody is familiar enough with g_sas to help me understand why the surface calculation method is not giving sensible values for these smaller ring systems. Also I am wondering if anybody can suggest any other free software that would allow me to compute van der Waal's and Solvent Excluded volumes. Thanks in advance. Jake Spooner -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
