[gmx-users] In-vacuo minimization of peptide

[Justin Lemkul]

On 6/29/17 8:29 AM, Apramita Chand wrote:
> 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?
> 

If you have one point, that's not a curve.  There's nothing to visualize, 
because mdrun already printed the value.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
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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