AMBER Archive (2008)

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

From: Sasha Buzko (obuzko_at_ucla.edu)
Date: Wed Nov 12 2008 - 18:53:06 CST

Hi all,
I have a little follow-up question to the earlier issue with apparently
evaporating water. I did re-image the trajectory with ptraj and also
tried an additional run with iwrap enabled. The result was pretty much
the same in both cases: the solvent shell was more or less fine, but the
protein ended up protruding from the side of the solvent box with about
half of it exposed.
Is it another imaging artefact associated perhaps with the fact that
only the last run was with iwrap=1? Or could it point at a problem with
parameters and the protein does indeed drift out of the solvent shell?

The input files are below.

Thanks very much

Sasha

steinbrt_at_rci.rutgers.edu wrote:
> Hi,
>
> what you see is probably atoms drifting out of the initial simulation box
> and sander does not automatically image them back in. Your system still
> corresponds to a densely packed waterbox, it's just a visualisation
> artifact stemming from periodic boundary conditions.
>
> If water really were boiling of (say because of a wrongly set
> thermostate), sander would crash with an error about box size changes.
>
> If you use ptraj to image your trajectories back after the MD run, you
> will see that every atom stayed within the initial box. The waters cant
> escape even if they try ;-)
>
> Regards,
>
> Dr. Thomas Steinbrecher
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
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>
> Input files:
>
> initial minimisation in 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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