AMBER Archive (2008)

Subject: AMBER: Origin of periodic box

From: Naser Alijabbari (na3m_at_virginia.edu)
Date: Wed Oct 15 2008 - 20:34:00 CDT

Dear community,

Here is a sample of my coordinates from a restart file:

 11.3821583 18.1661542 24.1323434 12.0606145 18.8372653 26.0152123

  11.5071003 18.9571744 26.9465253 12.8878889 17.5565535 26.1569275

  13.4276408 17.4890159 25.2123598 13.6155085 17.6783609 26.9593194

This is my periodic box information:

solvatebox 2trx TIP3PBOX 8

  Solute vdw bounding box: 32.421 37.765 37.628

  Total bounding box for atom centers: 48.421 53.765 53.628

I was wondering what the origin (0,0,0 = x,y,z) is for the above coordinates
or how are the coordinates assigned for each atom (I am guessing it can't be
the center of my box because then my 26.5 would be my largest coordinate,
and I would also have negative coordinate values which I don't see.)

Also I tried using the below commands to create a new restart file:

trajin bbprotein5.rst

center :1-108

image center familiar

trajout bbproteincntrd.rst restart

I thought this would only affect my coordinates but looking at the new
restart file my velocities are all zeroed. Can someone explain why?

For example I might have the following velocity information:

 -0.1213716 0.2252365 -0.1331371 0.4267375 -1.6400259 -0.0792864

   0.1190042 0.5353082 -0.3345033 -0.5339086 0.1233047 0.5253997

  -0.0889908 0.0161328 0.1234542 -0.3570667 -0.6634506 0.0428914

and the new restart velocities would be as follows:

   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000

   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000

   0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000

Thanks

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