From: faride badalkhani (farideh.khamseh_at_gmail.com)
Date: Thu Apr 14 2016 - 13:50:14 CDT
Since there is no crystallographic data for my structure (hyperbranched
polymers) I built the pdb file and then I performed the following steps:
1) Simulated annealing for the structure in vacuum from 300-700 and vice
versa, system remained in each step for 50 ps and after that MD simulation
for 1 ns
2) minimizing the system and water box for 25 ps followed by 100 ps MD in
NPT ensemble while rigid bonds was set to all
3) minimizing the system and water box for 25 ps followed by 100 ps MD in
NPT ensemble while rigid bonds was set to water
4) performing MD simulation for 600 ps in NPT
but when I want to perform production MD I get error.
p.s. according to
I added |MINx| + |MAXx|, |MINy| + |MAXy|, |MINz| + |MAXz| to determine
cell basis vectorsx, y, and z.
and all these simulations were performed with 0.5 fs time step.
When I look at the initial structure there is no strange thing, but if
these errors are related to initial structure what is the way to build .pdb
file for my structure?
Any help will be appreciated.
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