[gmx-users] about normal mode analysis

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Double precision result:
http://comments.gmane.org/gmane.science.biology.gromacs.user/62746

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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