leila karami wrote:
how can I do energy minimization with position restraint. how I creat
cooresponding mdp file? what should considered except what is seen in
below mdp file.
Reading the manual, wiki, and the many tutorials available will give you the
background you need. The obvious question comes to mind - did you try it?
-Justin
define = -DPOSRES
constraints = none
integrator = steep
nsteps = 100
emtol = 2000
emstep = 0.01
nstcomm = 1
ns_type = grid
rlist = 1
rcoulomb = 1.0
rvdw = 1.0
Tcoupl = no
Pcoupl = no
gen_vel = no
------------------------------------------------------------------------
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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