[gmx-users] Removing relative motion of water

Dear all: I'm trying to use g_densmap to analyze densities of water, but the result seems to be blurry due to relative motion (?). Does anyone have any suggestions on how to solve this problem? Thanks in advance. Happy holidays! Best, Wei-Hsiang -- Wei-Hsiang Weng (翁偉翔) Department of Life

[gmx-users] gmx bundle

Dear all: I'm trying to calculate kinks within alpha helices using gmx bundle. I specify 4 Ca atoms from the helix top, bottom and kink separately in the index file. And, I've used the option -na 1. But I keep getting the results shown below. @title "Kink angles" @xaxis label "Time

[gmx-users] g_correlation

Dear all: I'm using the generalized correlation analysis tool developed by Lange and Grubmüller. Does anyone know the option for setting the range of correlation values? Say, 0 to 1? Any advice would be appreciated, thanks in advance. Best, Wei-Hsiang -- Wei-Hsiang Weng (翁偉翔) Department of Life

[gmx-users] g_correlation

Dear all: Has anyone succeeded in installing the command g_correlation in GROMACS 4.5.5? File obtained from http://www.mpibpc.mpg.de/grubmueller/g_correlation I tried installing but I keep getting the error message seen below. *6/include -I/usr/local/gromacs/bin/include/gromacs -c -o

Re: [gmx-users] g_correlation

>>>>>>>>>>>>>>> Wei-Hsiang Weng (翁偉翔), Master Department of Life Sciences Tzu-Chi University, Taiwan 0975-232-245 (C) E-mail: weiweng...@gmail.com 104726...@gms.tcu.edu.tw 2015-12-10 16:45 GMT+08:00 Kutzner, Carsten <ckut...@gwdg.de>: > Hi, &