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

[NG HUI WEN]

Hi

Thanks a lot for the suggestions. 

I removed -DFLEXIBLE this time but it still didn't work unfortunately. I
started off with 0 distorted planar group and ended up with 38 after
minimization (same as before).

Justin, the values were as below when the minimization converged to
machine precision
Pot E= -1.6560090 e+04 (initial = 5.64598 e+09)
Max force = 2.8172894 e+02 (initial = 7.95313 e+11)
Norm of force = 2.9346647 e+01

HW


-----Original Message-----
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Justin A. Lemkul
Sent: Monday, September 20, 2010 7:07 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Energy Minimzation with Gromacs leads to
distortionof planar groups



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

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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