Kukol, Andreas wrote:
Try without -DFLEXIBLE.
See this message:
http://lists.gromacs.org/pipermail/gmx-users/2008-October/037571.html
Doesn't -DFLEXIBLE only affect water, not the aromatic rings of the protein?
Don't the real problems come from running actual MD with -DFLEXBILE? In some
cases for EM, it has even been recommended.
-Justin
Andreas
-----------------------
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Behalf Of NG HUI WEN
Sent: 20 September 2010 04:21
To: gmx-users@gromacs.org
Subject: [gmx-users] Energy Minimzation with Gromacs leads to distortion of
planar groups
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.
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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