[gmx-users] Re: Problem with minimizing the energy of the solvated system

[Justin A. Lemkul]

On 7/5/12 5:05 PM, jonas87 wrote:
> I'm following the tutorial exactly. Even have my files named the same way.
> The contents of my minil.mdp (pcb is changed from no to xyz right before
> running the energy minimazation of the solvated system):
>
> title		= Energy Minimization	; Title of run
> cpp		= /lib/cpp	; Preprocessor
> define          = -DFLEXIBLE
> integrator	= steep		; Algorithm (steep = steepest descent minimization)
> emtol		= 1.0		; Stop minimization when the maximum force < 1.0 kJ/mol
> nsteps		= 500		; Maximum number of (minimization) steps to perform
> nstenergy	= 1		; Write energies to disk every nstenergy steps
> energygrps	= System	; Which energy group(s) to write to disk
> ns_type		= simple	; Method to determine neighbor list (simple, grid)
> coulombtype	= cut-off	; Treatment of long range electrostatic interactions
> rcoulomb	= 1.0		; long range electrostatic cut-off
> rvdw		= 1.0		; long range Van der Waals cut-off
> constraints	= none		; Bond types to replace by constraints
> pbc		= no		; Periodic Boundary Conditions (yes/no)
>
>

You're probably losing the box information somewhere along the line while 
switching back and forth between .gro and .pdb.  The CRYST1 line in 
protein-solvated.pdb should agree with the previous settings.  If it doesn't, 
something has gone wrong.  I recall some previous version of Gromacs had issues 
reading and writing correct box vectors in .pdb files; I don't know which one. 
It's always safe to use .gro files for everything, though in principle, .pdb 
files should work as well.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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