> I am equilibrating the solvent (in solvated protein-ligand complex)
> using the following parameters.
> But at the end of heating phase itself (first 20 ps), after reimaging,
> I found that the solvent molecules forming many hollow spaces on the
> surfaces. MD runs seem to be stable and fine (temp, energy, density,
> please see the attached .out file).
Your heating phase (step 3) is constant volume. The next phase is constant
pressure (ntb=2) and thus should fix the vdw voids. E.g.
http://www.rosswalker.co.uk/tutorials/amber_workshop/Tutorial_one/section5.htm
for a discussion of vdw voids.
Bill
> **********
> step 1
> **********
> complex: initial minimization - solvent and ions
> &cntrl
> imin = 1,
> ntpr = 500,
> maxcyc = 10000,
> ncyc = 5000,
> ntb = 1,
> ntr = 1,
> cut = 12.0
> drms = 0.001
> /
> Hold the protein fixed
> 500.0
> RES 1 285
> END
> END
> ************
> step 2
> ***********
> bztcomplex: initial minimization -entire system
> &cntrl
> imin = 1,
> ntpr = 500,
> maxcyc = 5000,
> ncyc = 1000,
> ntb = 1,
> cut = 8.0
> drms = 0.001
> /
> *********
> step 3
> ***********
> complex: heating phase MD - solvent and ions
> &cntrl
> imin = 0,
> ntpr = 100,ntwx = 100, ntwr = 1000,
> nstlim = 20000,dt = 0.001,
> tempi = 0.0, temp0 = 300.0,
> ntb = 1,
> ntr = 1,
> cut = 10.0
> ntt = 3, gamma_ln = 1.0
> /
> Hold the protein fixed
> 10.0
> RES 1 285
> END
> END
> *********
> step 4
> *********
> bztcomplex: equilibration phase MD - solvent and ions
> &cntrl
> imin = 0,irest=1, ntx=7,
> ntb=2, pres0=1.0, ntp=1,
> taup=2.0,
> ntpr = 100,ntwx = 100, ntwr = 1000,
> nstlim = 20000,dt = 0.001,
> tempi =300.0, temp0 = 300.0,
> ntr = 1,
> cut = 10.0
> ntt = 3, gamma_ln = 1.0
> /
> Hold the protein fixed
> 10.0
> RES 1 285
> END
> END
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri May 14 2010 - 13:30:03 PDT
