[gmx-users] Energy minimization

[bharat gupta]

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
Mobile no. - 010-5818-3680
E-mail : monu46010 at yahoo.com
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