RE: how to calculate the box size

From: JC Gumbart (
Date: Tue Mar 06 2012 - 09:00:14 CST

And to further clarify, VMD reads them from the dcd and can be accessed

molinfo top get a (b and c)

-----Original Message-----
From: [] On Behalf
Of Axel Kohlmeyer
Sent: Tuesday, March 06, 2012 8:53 AM
To: Aron Broom
Cc: mjyang;
Subject: Re: namd-l: how to calculate the box size

On Tue, Mar 6, 2012 at 9:44 AM, Aron Broom <> wrote:
> 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.

that is nonsense. you cannot reconstruct the box size from the positions of
the atoms. full stop. but the box dimensions are usually stored in the dcd
trajectory file. those are the only ones you can use or those in a proper
.xsc file.


> On Tue, Mar 6, 2012 at 2:48 AM, mjyang <> wrote:
>> 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
> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo

Dr. Axel Kohlmeyer
College of Science and Technology
Temple University, Philadelphia PA, USA.

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