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

[Justin A. Lemkul]

NG HUI WEN wrote:
> 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
> 

I guess this all comes down to the definition of "distorted."  A planar group 
may not necessarily remain entirely planar during EM or MD.  It will be 
maintained by an improper dihedral (details in the manual), so some positions 
may fluctuate, but on average (during MD) the group should be planar.  If you've 
detected severe distortions (i.e., impossible geometry) then it might be worth 
additional investigation.  But given the fact that you've arrived at a 
reasonable potential and maximum force, I see nothing wrong with your results.

-Justin

> 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
>> <<
>> Email has been scanned for viruses by UNMC email management service
> 

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

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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