[gmx-users] Energy minimization

[Amit Choubey]

OK what seemed wrong to you?

On Mon, Jan 17, 2011 at 12:24 AM, bharat gupta <bharat.85.monu at gmail.com>wrote:

> I am doin the first minimization step.. here are the details of minim.mdp
> file
>
> ; minim.mdp - used as input into grompp to generate em.tpr
> ; Parameters describing what to do, when to stop and what to save
> integrator = steep  ; Algorithm (steep = steepest descent minimization)
> emtol  = 1000.0   ; Stop minimization when the maximum force < 1000.0
> kJ/mol/nm
> emstep          = 0.01          ; Energy step size
> nsteps  = 50000    ; Maximum number of (minimization) steps to perform
> ; Parameters describing how to find the neighbors of each atom and how to
> calculate the interactions
> nstlist  = 1  ; Frequency to update the neighbor list and long range forces
> ns_type  = grid  ; Method to determine neighbor list (simple, grid)
> rlist  = 1.0  ; Cut-off for making neighbor list (short range forces)
> coulombtype = PME  ; Treatment of long range electrostatic interactions
> rcoulomb = 1.0  ; Short-range electrostatic cut-off
> rvdw  = 1.0  ; Short-range Van der Waals cut-off
> pbc  = xyz   ; Periodic Boundary Conditions (yes/no)
>
>
>
> --
> Bharat
> Ph.D. Candidate
> Room No. : 7202A, 2nd Floor
> Biomolecular Engineering Laboratory
> Division of Chemical Engineering and Polymer Science
> Pusan National University
> Busan -609735
> South Korea
> Lab phone no. - +82-51-510-3680, +82-51-583-8343
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> E-mail : monu46010 at yahoo.com
>
>
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