**From:** Aron Broom (*broomsday_at_gmail.com*)

**Date:** Tue Mar 06 2012 - 08:44:57 CST

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What if for the water molecules in your system you calculate from the

center of mass of the waters rather than just the atomic coordinates? I

don't know what the real answer is, but that would shrink your box ever so

slightly.

On Tue, Mar 6, 2012 at 2:48 AM, mjyang <mjyang_at_hku.hk> wrote:

*> Dear NAMD users,
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*>
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*> I performed a simulation by NAMD for a protein system solvated by a
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*> cubic water box. Now I extracted the snapshots from NAMD trajectory for
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*> postpone analysis, in which the protein should be centered in the box. The
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*> box size was calculated by (max_x-min_x, max_y-min_y, max_z-min_z), where
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*> max_x,y,z and min_x, y, z are the maximum and minimum coordinate values of
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*> the extracted frame. However, the box size calculated in this way is a
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*> little larger than the real one, resulting in gaps in the recentered box.
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*> It seems that the box size written out by NAMD in the *.xsc file is better
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*> than what I calculated. But the NAMD output size (in *.xsc file) only
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*> corresponds to the last frame of a segment of trajectory file and I need
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*> the size for each frame in the traj. Could someone please tell me how NAMD
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*> calculate the box along MD simulations?
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*>
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*>
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*> Many thanks.
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*>
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*>
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*> Mingjun
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*>
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*>
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-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo

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