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Tutorial 1: Molecular dynamics simulation of protein

Energy minimization

We will run two stage energy minimization of our system. In the first stage we will minimize water positions keeping protein fixed. And in the second stage the whole system will be minimized. You should use control data files min1.in and min2.in when running sander (program which carries out energy minimization and molecular dynamics).

Here is the min1.in:

Information in the input file:
imin=1  perform minimization
maxcyc=5000  maximum number of minimization cycles
ncyc=2500  method of minimization will be switched from steepest descent to conjugate gradient after ncyc cycles
cut=10.0  specify the nonbonded cutoff, in Angstroms
ntb=1  periodic boundary, constant volume
ntc=1  SHAKE is not performed (for better energy convergence)
ntf=1  force evaluation, complete interaction is calculated
ntpr=10  every ntpr steps energy information will be printed in human-readable form to mdout file
ntr=1  flag for restraining specified atoms using harmonic potential
restraintmask=':1-500'  string that specifies the restrained residues
restraint_wt=2.0  the weight (in kcal/mol-A^2) for the positional restraints

So, run sander to perform minimization stage 1:

sander -O -i min1.in -p protein.prmtop -c protein.inpcrd -o protein_min1.out -r protein_min1.rst -ref protein.inpcrd

File usage:
mdin  control data for the min/md run
prmtop  molecular topology, force field, atom and residue names
inpcrd  initial coordinates
mdout  user readable state info and diagnostics
rstrt  final coordinates and velocities
refc  reference coords for position restraints

Here is the min2.in:

Use min2.in and protein_min1.rst to run minimization stage 2:

sander -O -i min2.in -p protein.prmtop -c protein_min1.rst -o protein_min2.out -r protein_min2.rst

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