leila karami wrote:
dear chris
I did EM :
Steepest Descents did not converge to Fmax < 2000 in 101 steps.
Potential Energy = -3.2421097e+05
Maximum force = 1.4766100e+04 on atom 1441
Norm of force = 2.5146213e+02
I am sure that constraints=none during EM.
how do I increase the LINCS/SHAKE iterations to the appropriate number?
this is my em.mdp file
The better approach is to run more than 100 steps of EM. Your force is still
unacceptably high, which is likely what is causing the crash you see later.
-Justin
cpp = /usr/bin/cpp
define = -DFLEX_SPC
constraints = none
integrator = steep
nsteps = 100
;
; Energy minimizing stuff
;
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
--
========================================
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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