On 4/19/13 1:18 PM, Shima Arasteh wrote:
Lets check the minim.mdp settings:
( ff applied is charmm36)
define = -DPOSRES
integrator = steep
emtol = 100.0
emstep = 0.01
nsteps = 50000
nstlist = 1
ns_type = grid
rlist = 1.2
rlistlong = 1.4
coulombtype = PME
rcoulomb = 1.2
rvdw = 1.2
vdwtype = switch
rvdw_switch = 1.0
pbc = xyz
I would be grateful for your suggestions.
I see no reason to use restraints (doing so defeats the purpose of EM), but
otherwise the settings are fine.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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