NG HUI WEN wrote:
Dear Gmxusers,
I have noticed that energy minimization with gromacs (gromos G53a6
forcefield) had led to the distortion of sidechain planarity in my
protein model. Comparison of PROCEHCK results between the pre- and post
energy minimized structures have shown an increase in the number of
distorted planar groups (e.g. rings and non-ring aliphatic groups).
As steepest descent seem to converge very rapidly (<500 steps) to
machine precision, I also tried using the conjugate gradient and lbfgs
methods.
What were the values of the potential and maximum force when EM converged?
-Justin
The .mdp files used are as follow.
Steepest descent
title = Energy Minimization without position restraint
cpp = /lib/cpp ; Preprocessor
define = -DFLEXIBLE
; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent
minimization)
emtol = 1.0 ; Stop minimization when the maximum force < 1.0
kJ/mol
nsteps = 500 ; Maximum number of (minimization) steps
to perform
nstenergy = 1 ; Write energies to disk every nstenergy steps
energygrps = System ; Which energy group(s) to write to disk
; Parameters describing how to find the neighbors of each atom and how
to calculate the interactions
ns_type = simple ; Method to determine neighbor list
(simple, grid)
coulombtype = cut-off ; Treatment of long range electrostatic interactions
rcoulomb = 1.0 ; long range electrostatic cut-off
rvdw = 1.0 ; long range Van der Waals cut-off
constraints = none ; Bond types to replace by constraints
pbc = no ; Periodic Boundary Conditions (yes/no)
CG
title = Energy Minimization with out position restraint
cpp = /lib/cpp ; Preprocessor
define = -DFLEXIBLE
; Parameters describing what to do, when to stop and what to save
integrator = cg ; Algorithm (steep = steepest descent minimization)
emtol = 1.0 ; Stop minimization when the maximum force < 1.0
kJ/mol
dt = 0.0001
nsteps = 500 ; Maximum number of (minimization) steps
to perform
nstenergy = 1 ; Write energies to disk every nstenergy steps
energygrps = System ; Which energy group(s) to write to disk
; Parameters describing how to find the neighbors of each atom and how
to calculate the interactions
ns_type = simple ; Method to determine neighbor list
(simple, grid)
coulombtype = cut-off ; Treatment of long range electrostatic interactions
rcoulomb = 1.0 ; long range electrostatic cut-off
rvdw = 1.0 ; long range Van der Waals cut-off
constraints = none ; Bond types to replace by constraints
pbc = no ; Periodic Boundary Conditions (yes/no)
lbfgs
title = Energy Minimization without position restraint
cpp = /lib/cpp ; Preprocessor
define = -DFLEXIBLE
; Parameters describing what to do, when to stop and what to save
integrator = l-bfgs ; Algorithm (steep = steepest descent
minimization)
emtol = 1.0 ; Stop minimization when the maximum force < 1.0
kJ/mol
nsteps = 1500 ; Maximum number of (minimization)
steps to perform
nstenergy = 1 ; Write energies to disk every nstenergy steps
energygrps = System ; Which energy group(s) to write to disk
; Parameters describing how to find the neighbors of each atom and how
to calculate the interactions
ns_type = simple ; Method to determine neighbor list
(simple, grid)
coulombtype = pme ; Treatment of long range electrostatic interactions
rcoulomb = 1.2 ; long range electrostatic cut-off
vdwtype = switch
rlist = 1.2
rvdw = 1.0 ; long range Van der Waals cut-off
rvdw-switch = 0.8
constraints = none ; Bond types to replace by constraints
pbc = xyz ; Periodic Boundary Conditions (yes/no)
I might have done something wrongly to cause this. Would really
appreciate it if someone could enlighten me on this.
Thanks!!
HW
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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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