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

[Justin A. Lemkul]

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-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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-- 
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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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