[gmx-users] In-vacuo minimization of peptide

[Apramita Chand]

Dear All,
I have constructed the initial structure of peptide using Pymol and
energy-minimizing it using steepest-descent algorithm(both with and without
restraints) with the conditions:
integrator = steep ; Algorithm (steep = steepest descent
minimization)
emtol = 1000.0 ; Stop minimization when the maximum force <
10.0 kJ/mol
nsteps = 1000 ; Maximum number of (minimization) steps to
perform
nstenergy = 1 ; Write energies to disk every nstenergy
steps
energygrps = Protein ; Which energy group(s) to write to disk
; Parameters describing how to find the neighbors of each atom and how to
calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list
ns_type = grid ; Method to determine neighbor list (simple,
grid)
coulombtype = PME ; Treatment of long range electrostatic
interactions
rlist = 0.9 ; Cut-off for making neighbor list (short
range forces)
rcoulomb = 0.9; long range electrostatic cut-off
rvdw = 1.4 ; long range Van der Waals cut-off
constraints = none ; Bond types to replace by constraints
pbc = xyz ; Periodic Boundary Conditions (yes/no)

With position restraints , it converges in just 12 steps and gives energy as
Steepest Descents converged to Fmax < 1000 in 12 steps
Potential Energy  = -1.4251520e+02
Maximum force     =  7.4820624e+02 on atom 29
Norm of force     =  3.1645233e+02

Without position restraints, it converges in just 1 step

Steepest Descents converged to Fmax < 1000 in 1 steps
Potential Energy  = -1.3968005e+02
Maximum force     =  9.3205127e+02 on atom 27
Norm of force     =  4.1683670e+02

The potential energy curve is blank when I see energy.xvg.


Is there something I might be doing wrong?


yours sincerely,
Apramita