[gmx-users] about normal mode analysis

[Justin Lemkul]

On 2/6/14, 9:27 AM, Gmail2 wrote:
> Double precision result:
> http://comments.gmane.org/gmane.science.biology.gromacs.user/62746
>

I assume you mean to say that you're having the same issue as described in that 
thread?  You'll note that Michael mentions the existence of a bug, which has 
since been fixed (http://redmine.gromacs.org/issues/1308).

Update your Gromacs version and try again.  The 4.5.x series is quite old at 
this point.

-Justin

> Ahmet Yıldırım
>
>
> 6 Şub 2014 tarihinde 15:39 saatinde, Justin Lemkul <jalemkul at vt.edu> şunları yazdı:
>
>>
>>
>>> On 2/6/14, 8:25 AM, Ahmet yıldırım wrote:
>>> Dear users,
>>>
>>> I'm trying to do NMA of a structure. When I minimize a structure:
>>>
>>> Polak-Ribiere Conjugate Gradients converged to Fmax < 10 in 3742 steps
>>> Potential Energy  = -5.2965824e+04
>>> Maximum force     =  8.0245171e+00 on atom 3038
>>> Norm of force     =  1.3228445e+00
>>>
>>> When I try to perform a normal mode analysis:
>>> Maximum force: 8.71126e+02
>>> Maximum force probably not small enough to ensure that you are in an
>>> energy well. Be aware that negative eigenvalues may occur when the
>>> resulting matrix is diagonalized.
>>>
>>> I've seen some comments on this but I couldnt find any thing about its
>>> solution. Anyone could give me any suggestions? Are there anyting wrong
>>> with my input files?
>>
>> It appears you are using single precision.  You should be using double precision for NMA.
>>
>> -Justin
>>
>>> By the way, I am using Gromacs 4.5.5.
>>>
>>> Commands:
>>> pdb2gmx -f protein.pdb -o protein.gro -p protein.top
>>> 14: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
>>> Select the Water Model:
>>> 4: SPC    simple point charge
>>>
>>> editconf -f protein.gro -o protein-solvated.gro -bt dodecahedron -d 1.0
>>>
>>> grompp -v -f minim.mdp -c protein-solvated.gro -p protein.top -o
>>> protein-EM-solvated.tpr
>>> mdrun -v -deffnm protein-EM-solvated
>>>
>>> grompp -v -f nm.mdp -c protein-EM-solvated.gro -p protein.top -o
>>> protein-nm.tpr
>>> mdrun -v -deffnm protein-nm
>>>
>>> Input files:
>>>
>>> minim.mdp:
>>> integrator    = cg        ; Algorithm (steep = steepest descent
>>> minimization)
>>> emtol        = 10.0      ; Stop minimization when the maximum force <
>>> 1000.0 kJ/mol/nm
>>> emstep          = 0.01          ; Energy step size
>>> nsteps        = 100000      ; Maximum number of (minimization) steps to
>>> perform
>>>
>>> ; Parameters describing how to find the neighbors of each atom and how to
>>> calculate the interactions
>>> nstlist        = 0        ; Frequency to update the neighbor list and long
>>> range forces
>>> rlist        = 0        ; Cut-off for making neighbor list (short range
>>> forces)
>>> rcoulomb    = 0        ; Short-range electrostatic cut-off
>>> rvdw        = 0        ; Short-range Van der Waals cut-off
>>> pbc        = no         ; Periodic Boundary Conditions (yes/no)
>>> constraints     = none
>>>
>>> nm.mdp:
>>> integrator    = nm
>>> nsteps          = 500000  ; 1ns
>>> dt              = 0.002     ; 2 fs
>>>
>>> ; Parameters describing how to find the neighbors of each atom and how to
>>> calculate the interactions
>>> nstlist        = 0        ; Frequency to update the neighbor list and long
>>> range forces
>>> rlist        = 0        ; Cut-off for making neighbor list (short range
>>> forces)
>>> rcoulomb    = 0        ; Short-range electrostatic cut-off
>>> rvdw        = 0        ; Short-range Van der Waals cut-off
>>> pbc        = no         ; Periodic Boundary Conditions (yes/no)
>>> constraints    = none
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 601
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================