rob yang wrote:
Dave,
I am using it for visualization for now. -pbc mol gave me the same output as
-pbc whole, which was a cubic box with broken protein. -pbc atom gave the
dodecahedron box and intact protein. But since the functionality of -pbc mol
has changed, and may not be applicable to visualization purposes, it is then
not a bug.
Judging from your reply, I seem to get the feeling that -pbc atom might not be a wise idea later on if I do actual analysis of the MD trajectory.
that is correct.
but -pbc mol -ur compact should give you a dodecahedron but with intact
molecules. If you have an example where -pbc mol gives you a broken
molecule that is a bug, unless the protein was broken from the
beginning, which it shouldn't be. If this is indeed the case then please
submit a bugzilla.
----------------------------------------
Date: Fri, 7 Mar 2008 16:50:50 +0100
From: [EMAIL PROTECTED]
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] trjconv behaving differently in 3.3.3 vs previous
versions
"did not work" is not good enough a description. However, the
functionality has changed, intentionally. The -pbc atom breaks molecules
and should be used with care (for visualization only). So hence I
presume this is not a bug.
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David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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