From: Ramon Mendoza Uriarte (
Date: Sun Mar 21 2021 - 00:57:03 CDT

Hello Ashar and Axel,

Thank you to the both of you for your comments. I was not aware the coordinates would change depending on the machine or to precession. I would have thought the coordinates would be unchanging once the output was written.

Thank you,
From: Ashar Malik <>
Sent: Saturday, March 20, 2021 10:20 PM
To: Ramon Mendoza Uriarte <>
Subject: Re: vmd-l: Why do the coordinates of my atoms change when writing to a pdb file?

Hi Ramon,

This is related to precision.
Was the coor file generated on the same computer? If you stick with the same machine this will not happen.

Depending on what you are doing - this may or may not be ignorable.


On Sun, Mar 21, 2021 at 12:31 PM Ramon Mendoza Uriarte <<>> wrote:
Hello VMD Community,

I loaded a molecule with its respective .psf and .coor files, where the .coor file was read as a NAMD Binary Coordinates file. I then wanted to write out the pdb file; for example, by doing the following in the TkConsole:

set all [atomselect top "all"]
$all writepdb new.pdb

However, I found it surprising that this yields slightly different coordinates and box dimensions. For instance:

>From .coor: (-12.171550750732422, 5.363558769226074, -15.094483375549316), (-11.626058578491211, 4.931212425231934, -15.867215156555176),
                      (-12.769146919250488, 6.002536773681641, -15.656786918640137) <--- A small subset of all the coordinates
                      cellBasisVector1 87.59627914428711 0 0
                      cellBasisVector2 0 88.96563339233398 0
                      cellBasisVector3 0 0 97.37928009033203
                      cellOrigin 0.1676909178495407 0.361166387796402 0.04699717089533806

>From new.pdb: (-12.17199993133545, 5.363999843597412, -15.093999862670898), (-11.62600040435791, 4.931000232696533, -15.866999626159668),
                            (-12.769000053405762, 6.002999782562256, -15.656999588012695) <--- A small subset of all the coordinates
                            cellBasisVector1 87.59599685668945 0 0
                            cellBasisVector2 0 88.96599960327148 0
                            cellBasisVector3 0 0 97.37999725341797
                            cellOrigin 0.16769009828567505 0.36116769909858704 0.04699849709868431

So far, I have tried a Google and VMD archive search; however, I have not determined why this occurred. Additionally, I am using VMD for LINUXAMD64, version 1.9.4a51. Any comments on why this occurred would be appreciated.

Thank you,