Re: how to calculate the box size

From: Cristhian Boetsch (
Date: Tue Mar 06 2012 - 10:48:30 CST

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.

2012/3/6 mjyang <>:
> 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

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:21:18 CST