AMBER Archive (2008)

Subject: Re: AMBER: Problem with evaporating water over longer simulation times

From: Gustavo Seabra (gustavo.seabra_at_gmail.com)
Date: Wed Nov 12 2008 - 13:48:01 CST

Try adding 'iwrap=1' to your &cntrl namelist.

Gustavo.

On Wed, Nov 12, 2008 at 2:14 PM, Sasha Buzko wrote:
> Hi all,
> When simulating proteins in explicit solvent, I noticed that after a while
> water molecules start "boiling off" the protein. The result is a large and
> diffuse solvent cloud that becomes apparent after 5-10 ns of simulated time.
>
> First, I noticed it in some of my runs, but then exactly the same problem
> appears to be present in one of the tutorial simulations
> (http://ambermd.org/tutorials/advanced/tutorial3/section2.htm). If you
> download the resulting trajectory and display water, the solvent shell
> starts evaporating after a couple of nanoseconds.
>
> After I run a simulation for 20 ns with these parameters, the solute remains
> completely solvent-free and all water boils off into space. Just for the
> sake of completeness, I'm giving below the input files for all stages of my
> simulation.
> While the tutorial example uses somewhat different input, the solvent
> behavior is the same.
>
> Any thoughts would be very much appreciated.
>
> Thank you
>
> Sasha
>
>
>
> Input files:
>
> initial minimisation solvent
> &cntrl
> imin = 1,
> maxcyc = 5000,
> ncyc = 2500,
> ntb = 1,
> ntr = 1,
> cut = 15
> /
> Hold the protein fixed
> 500.0
> RES 1 242
> END
> END
>
> initial minimisation whole system
> &cntrl
> imin = 1,
> maxcyc = 5000,
> ncyc = 2500,
> ntb = 1,
> ntr = 0,
> cut = 15
> /
>
> Equilibration
> protein: 20ps MD
> &cntrl
> imin = 0,
> irest = 0,
> ntx = 1,
> ntb = 1,
> cut = 15,
> ntr = 1,
> ntc = 2,
> ntf = 2,
> tempi = 0.0,
> temp0 = 300.0,
> ntt = 3,
> gamma_ln = 1.0,
> nstlim = 10000, dt = 0.001,
> ntpr = 100, ntwx = 100, ntwr = 1000
> /
> Keep protein fixed with weak restraints
> 10.0
> RES 1 242
> END
> END
>
>
> Production MD
> Production simulation
> &cntrl
> imin = 0, irest = 1, ntx = 7,
> ntb = 2, pres0 = 1.0, ntp = 1,
> taup = 2.0,
> cut = 15, ntr = 0,
> ntc = 2, ntf = 2,
> tempi = 300.0, temp0 = 300.0,
> ntt = 3, gamma_ln = 1.0,
> nstlim = 250000, dt = 0.001,
> ntpr = 500, ntwx = 500, ntwr = 1000
> /
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