abdullah ahmed wrote:
Thank you for your reply,
Settings:
I am using the procedure outline by the "speptide" tutorial (i.e.
pdb2gmx, followed by editconf, genbox, grompp, and mdrun). The ".mdp"
file I've used is as follows:
; User spoel (236)
; Wed Nov 3 17:12:44 1993
; Input file
;
cpp = /usr/bin/cpp
define = -DPOSRES
constraints = none
integrator = steep
nsteps = 100
;
; Energy minimizing stuff
;
emtol = 20
emstep = 0.01
nstcgsteep = 10
nstcomm = 1
ns_type = grid
rlist = 1
rcoulomb = 1.0
rvdw = 1.0
Tcoupl = no
Pcoupl = no
gen_vel = no
coulombtype = PME
Force field: Encad all atom force field, using full sovent charges.
Local geometry is identical with the exception of the second charged
residue, which is replaced by Leucine in one structure.
Well, all you've done is a simple, restrained energy minimization, which won't
tell you much about anything. I don't see much point in using restraints during
EM anyway. Running real, unrestrained MD and obtaining suitable averages for
energies is the only way to make the conclusions I think you're after.
-Justin
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--
========================================
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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