**From:** Cristhian Boetsch (*cristhian.boetsch_at_gmail.com*)

**Date:** Tue Mar 06 2012 - 10:48:30 CST

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Hi Mingjun:

there is a comand `xstFreq 1000`. If you set this comand together

with a frecuency same as dcdFreq you can output the vectors of the box in a

a xst file.

Cristhian

2012/3/6 mjyang <mjyang_at_hku.hk>:

*> Dear NAMD users,
*

*>
*

*> I performed a simulation by NAMD for a protein system solvated by a
*

cubic water box. Now I extracted the snapshots from NAMD trajectory for

postpone analysis, in which the protein should be centered in the box. The

box size was calculated by (max_x-min_x, max_y-min_y, max_z-min_z), where

max_x,y,z and min_x, y, z are the maximum and minimum coordinate values of

the extracted frame. However, the box size calculated in this way is a

little larger than the real one, resulting in gaps in the recentered box.

It seems that the box size written out by NAMD in the *.xsc file is better

than what I calculated. But the NAMD output size (in *.xsc file) only

corresponds to the last frame of a segment of trajectory file and I need

the size for each frame in the traj. Could someone please tell me how NAMD

calculate the box along MD simulations?

*>
*

*>
*

*> Many thanks.
*

*>
*

*>
*

*> Mingjun
*

*>
*

-- Mic. Cristhian Boetsch Universidad Nacional de Río Cuarto Río Cuarto - Argentina Cel.: 0358-154361332

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