VMD-L Mailing List
From: sunyeping (sunyeping_at_aliyun.com)
Date: Thu Dec 25 2014 - 03:46:36 CST
------------------------------------------------------------------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 ?
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,
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.
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