Dear Prof. Roitberg,
Yes, with the imagining the system with its neighboring boxes, i see the the
holes on corners.
I just went over the threads very quickly. Someone wondered if ibelly can
cause the problem.
Do you think it is because of *ibelly*? I did use *ibelly* to fixed the
protein atoms positions for the first step of energy
minimization and then I did that MD run which shows the water holes.
I intend to run a large system (with large dimensions) in NVT ensemble. I
used Xleap to randomly
add the water molecules. Is it because Xleap is not be able to assign water
molecules with correct
density and cause this water hole? This not enough number of water molecule
cause free volume
when the system is large and form the water hole?
Thanks for your help very much!
Tom
On 5/25/10, Adrian Roitberg <roitberg.qtp.ufl.edu> wrote:
>
> What are seeing is a 'bubble'.
>
> Try imagining the system with its neighboring boxes and you will see a
> 'hole' instead of a funny shape.
>
> This simply means that you had too much volume for the amount of water you
> had originally, so water decided to have the correct density itself,
> regardless of the box.
>
> There are numerous threads in the list over the years, but what you need to
> is to be VERY carefully minimizing, heating and changing from to NPT very
> slowly, restraining the protein, the water, and releasing them.
>
> Adrian
>
>
>
> On 5/24/10 10:58 PM, Tom Williams wrote:
>
>> Dear All,
>>
>> I ran a MD of a case soaking a protein molecule with Sander in a
>> rectangle
>> PBC box,
>> but finally the result on file *.rst, are totally with not a rectangle
>> box. The are 4 missing parts
>> at the 4 corners of the projection of all the atoms in the the X,Y
>> directions.
>> In the direction of X, Z, the projection is still with rectangle shape.
>> Pls
>> see the attached
>> projected images. (Water atoms are red; protein atoms are blue).
>>
>> I don't think it is because of the PBC images because all the atoms look
>> still to be within the area of this rectangle box and my protein is at the
>> center of the box.
>> Can anyone help explain this strange solvation box shape?
>>
>> The following is the details:
>> ----------------------------------------
>> I ran a simple case of soaking a protein molecule in a rectangle box:
>> solvatebox LYZ TIP3PBOX 27
>>
>> My system is with big dimensions. In the file
>> of *.inpcrd, the bottom line states:
>> 107.0781340 101.4056200 99.1742170 90.0000000 90.0000000 90.0000000
>>
>> I ran MD with Sander
>>
>> 0-300K constant temp MD
>> &cntrl
>> imin=0,
>> ntb=1,cut=18.0,
>> ntc=2, ntf=2,
>> tempi=0.0, temp0=300.0,
>> ntt=1,iwrap=1,
>> nstlim=10000, dt=0.002,
>> ntpr=500, ntwx=1000
>> /
>>
>> Thanks for your help!
>>
>> Tom
>>
>>
>>
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>
> --
> 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 Mon May 24 2010 - 21:00:03 PDT
