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

[Justin A. Lemkul]

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
> 
> <<
> 
> Email has been scanned for viruses by UNMC email management service 
> <http://www.nottingham.edu.my>
> 
>  >>
> 

-- 
========================================

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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