VMD-L Mailing List

From: sunyeping (sunyeping_at_aliyun.com)
Date: Thu Dec 25 2014 - 03:46:36 CST

helllo ------------------------------------------------------------------发件人：Bahaa Mostafa <bmostafa_at_sci.cu.edu.eg>发送时间：2014年12月25日(星期四) 15:20收件人：Ashar Malik <asharjm_at_gmail.com>抄　送：vmd-l <vmd-l_at_ks.uiuc.edu>主　题：Re: vmd-l: non-bonded interactions thank you ashar for interest,but i don't use NAMD, i can't install it on my PC (windows) at all, i have VMD installed correctly, but i don't know if it calculates energy with charmm force field,so i have to do calculations myself, i think all terms are going well, till now but the nonbonding terms, i think some missing information about them cause my calculations not accurate, hope you can answer my question or recommend me a source to answer it, my question again :   some atoms have 1-4 LJ parameters , but others don't have,  what does it mean ? does it mean these atoms have no vdW interaction?,  or does it mean i should use the not 1-4 LJ parameters instead of these missing parts ? best wishes,  On Wed, Dec 24, 2014 at 2:43 PM, Ashar Malik <asharjm_at_gmail.com> wrote:  how can i calculate 1-4 vdW interaction energies for those atoms don't have 1-4 LJ parameters,  Three things:  1) You need to do some reading about what the force field terms are and what do they actually mean? 2) What 1 - 4 means? 3) When you run a simulation/minimization energy terms are printed out to the log file. vdW is a form of NONBONDED energy and has its own column. If you want to do the calculation not on the entire system but a small selection of atoms - look at ATOMSELECT to make the selection and use NAMDENERGY to calculate the energy of your system.   Hope this helps. -- Best,/A Disclaimer: This E-mail represents the views of its author only and does not necessarily reflect the opinions of Faculty of Science (SCI). We do not assume responsibility for any loss, damage (including direct, indirect, punitive, special, or consequential loss or damage), which you may directly or indirectly suffer from this email or its contents or through the ways of handling this email which includes sending, receiving, replying, forwarding, deleting, saving or changing and adjusting its content in any way. The existence of SCI logo on any material you receive means that it has been uploaded on the network servers, and does not necessarily mean that SCI owns these materials either partially or fully. In addition, any service that is provided by and/or through ITU(SCI), without exception, does not take any responsibility for any illegal use through them either by negligence, misconduct, misuse and/or abuse. And even though our network checks and scans all e-mails to make sure it is safe and does not contain any viruses,Trojans or Spywares , it is also the responsibility of the recipient to ensure that the e-mails and attachments therein are free of any danger, and SCI will take no responsibility for any damages or losses that may arise as a result from the misuse or the presence of viruses or spyware sent through messages or web services.