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

[NG HUI WEN]

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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