ahmet yıldırım wrote:
Dear Justin,
Thanks for your reply. You said "....You should avoid ad hoc changes."
You used different parameters for energy minimization at tutorial called
"Tutorial 5: Protein-Ligand Complex".
_*a part of your em.mdp*_
nstlist = 1
rlist = 1.0
rcoulomb = 1.0
rvdw = 1.0
_*a part of your md.mdp*_
nstlist = 5
rlist = 0.9
rcoulomb = 0.9
rvdw = 1.4
Then, Why did you change some parameters (nstlist,rlist,rcoulomb,rvdw)
for energy minimization?
In my experience, the outcome of EM is not particularly sensitive to those types
of changes for very robust systems, especially in single precision. The energy
values and maximum forces achieved don't change appreciably in most cases.
Regarding nstlist, for EM it should be set to 1.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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