RE: how to calculate the box size

From: mjyang (
Date: Wed Mar 07 2012 - 01:27:17 CST

Dear all,

   Thanks so much for all the insightful discussions. It seems that the best choice is the one read from trajectory files. I also monitored the distance between any two atoms in the recentered box and no unphysical values observed. In addition, the gap also disappeared. This is ok for my use of an initial configuration of the quantum calculations.

Many thanks.

Best regards.

From: [] On Behalf Of Norman Geist []
Sent: Wednesday, March 07, 2012 3:01 PM
To: 'Cristhian Boetsch'
Cc: Namd Mailing List
Subject: AW: namd-l: how to calculate the box size

I agree with Axel. Determining the box size even from a wrapped dcd by measuring min-max isn’t correct as one don’t respect the cell center used to create the data and will get a slightly dancing origin of the unit cell. By the way this method is called bounding box. One can easily check that with vmd when using the following command:

pbc box –center bb

and then play over the frames.

I would also advice to just use the box information namd wrote to the dcd, what is actually really great as one have the whole history of the box size over time and can even watch the box shrinking during pressure runs. Actually this fulfills all dreams one can have about the box information.

Best wishes

Norman Geist.

Von: [] Im Auftrag von Cristhian Boetsch
Gesendet: Dienstag, 6. März 2012 17:49
An: mjyang
Betreff: Re: namd-l: how to calculate the box size

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

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