[gmx-users] Energy Minimzation with Gromacs leads to distortion of planar groups

[Kukol, Andreas]

Try without -DFLEXIBLE.

See this message: http://lists.gromacs.org/pipermail/gmx-users/2008-October/037571.html

Andreas

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From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of NG HUI WEN
Sent: 20 September 2010 04:21
To: gmx-users at 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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