Re: [gmx-users] how to use the triplets index file generated by g_hbond

The first entry in summary_HBmap.dat is index zero (i.e., the "bottom" of the plot area). So the results look fine to me. -Justin On 5/14/12 1:02 PM, Yun Shi wrote: Hi Justin, Thank you for the perl script. But I wonder now why there is a difference between what shows in the hbmap.xpm file

Re: [gmx-users] how to use the triplets index file generated by g_hbond

Hi Justin, Thank you for the perl script. But I wonder now why there is a difference between what shows in the hbmap.xpm file and the summary_HBmap.dat generated. For example, I found many occurrences of the second to last H-bond in the 20hbmap.xpm file attached (visualized by GIMP), but in the s

Re: [gmx-users] how to use the triplets index file generated by g_hbond

On 5/5/12 1:22 PM, Yun Shi wrote: Hello all, I have used g_hbond with -hbn option to generate a .ndx file that has Acceptor - Donor - Hydrogen in each line of the last index group. But I wonder I could I use this index file to monitor each hydrogen bond specified by these triplets along the t

[gmx-users] how to use the triplets index file generated by g_hbond

Hello all, I have used g_hbond with -hbn option to generate a .ndx file that has Acceptor - Donor - Hydrogen in each line of the last index group. But I wonder I could I use this index file to monitor each hydrogen bond specified by these triplets along the trajectory? Also, I understand that th