I believe you should try to go through the tutorials in the amber web page.
What you are seeing is a centering issue, the protein is not in the
center of the box.
Since you are using periodic boundary conditions, there is NO real box,
just images, so your molecule is NOT protruding outside the box as in
'part of it is in vaccum', it is simply spilling onto the neighbor box.
Adrian
Sasha Buzko wrote:
> 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.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
>> /
>
>
--
Dr. Adrian E. Roitberg
Associate Professor
Quantum Theory Project
Department of Chemistry
Senior Editor. Journal of Physical Chemistry
American Chemical Society
University of Florida PHONE 352 392-6972
P.O. Box 118435 FAX 352 392-8722
Gainesville, FL 32611-8435 Email adrian.qtp.ufl.edu
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Received on Fri Dec 05 2008 - 14:36:23 PST
