VMD-L Mailing List

From: hamid mosaddeghi (hamid592004m_at_yahoo.com)
Date: Wed Aug 31 2011 - 01:23:37 CDT

Dear Hitesh   I counted Hbond from VMD for SPC/E water model in normal condition , I got 2.56 Hbond per/molcule but more paper reported 3.~ 3.3 Hbond per/molcule why?   I used Cutoff angle 30 and cutoff distance 3.5 A from literatures.   Best regards   Hamid Mosaddeghi   Phd Student Of Physical Chemistry . ----- Forwarded Message ----- From: Hitesh Patel <hiteshpatel379_at_gmail.com> To: vmd-l_at_ks.uiuc.edu Sent: Tuesday, August 30, 2011 9:17 PM Subject: vmd-l: Hbonds for a specific frame Hello VMD Users, I am writing script for counting HBonds. I am able to count but, It is for one displayed frame. What is the command to count hbonds for specific frame? So, I can change the frame number in loop. Thanks, -Hitesh