VMD-L Mailing List

From: sarah k (dailycolors_at_gmail.com)
Date: Mon Dec 14 2009 - 23:37:02 CST

dear Yu,

your supervisor is so knowledgeable but I'm not. when you run your steered
simulation by namd graphical interface, it does minimization and you can
choose to it results in some binary output files, too. i think you should
council with someone professional in physical chemistry to decide which of
the three ones to choose. i don't have enough information to guide you.

when you run paratool, after the edition of atom types, you autogenerate all
the coordinates. there some values for most of the bonds and etc are lost.
in the window you can see a bottom saying something like guess using analog
parameters (i can't access my pc now to tell you the exact phrase). you can
highlight them one by one and use analog parameters.

i used CHARMM, too. the result didn't seem logical. you'd better continue
using the VMD. my project was finished last night and the rsmd plot and
comparisons of the results before and after using namd showed that the
results are acceptable. so you can go on doubtless. all the computational
softwares available just produce errors, not always because of bugs. you
should just be careful about all the subprograms available and following the
guidelines correctly.

enjoy life,
Sarah