From: Jacqueline Schmidt (jacqueline_schmidt_1983_at_yahoo.com)
Date: Wed Oct 03 2012 - 10:32:37 CDT
Thanks Aron for your respond,
I actually find the way to do it by:
molinfo $molid get a (/b/c)
From: Aron Broom <broomsday_at_gmail.com>
To: Jacqueline Schmidt <jacqueline_schmidt_1983_at_yahoo.com>
Cc: namd <namd-l_at_ks.uiuc.edu>
Sent: Wednesday, October 3, 2012 11:19 AM
Subject: Re: namd-l: box dimension for unwrapped boxes?
I think that either way is a just a post-processing problem. I think it's generally better to wrap the coordinates and when making a movie or something, just keep the peptide centered in each frame. This way the coordinates for each atom can't become too large (although maybe this isn't an issue with the binary DCD format).
Anyway, for your problem, I think the box dimensions for re-wrapping are actually written inside the DCD file, and so there is a convenient method for wrapping them with VMD. I could be wrong about that, but I suggest searching through the mailing list, as this problem comes up somewhat regularly.
On Wed, Oct 3, 2012 at 11:14 AM, Jacqueline Schmidt <jacqueline_schmidt_1983_at_yahoo.com> wrote:
Dear Namd users,
>I have ran several simulations in NPT ensemble and I did not wrap the molecules b/c I wanted to get smooth movement of the peptide (for making nice movies from the simulation results). Now I want to get some density distributions from some the system species but I have encounterd with the problem than I should wrap back the coordinated in order to get the distribution plots (I need exact box dimension for that purpose). However, since the simulation has been run in NPT, the size of the box changes and because I did not wrap the molecucles in the simulation the "measure minmax" can not give me the box dimension anymore!!!
>Also in the standard namd output, I can see that the volume is reported but not the dimensions in x, y, z
>can anyone please help? can I use these simulations to these density distributions??
>looking forward to hearing something positive!!
Aron Broom M.Sc
Department of Chemistry
University of Waterloo
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