Okay, my mistake. Here's what each option gave me (all with -ur compact):
-pbc whole: broken protein, rectangular box
-pbc mol: intact protein, rectangular box, part of protein sticking outside the
box
-pbc atom: intact protein, dodecahedron box
> but -pbc mol -ur compact should give you a dod
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 shou
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
molecules
and should be used with care (for visualization only). So hence I
presume this is not a bug.
-Rob
Date: Fri, 7 Mar 2008 07:42:41 +0100
From: [EMAIL PROTECTED]
To: gmx-users@gromacs.org
Subject: Re: [gmx-users] trjconv behaving differently i
> Subject: Re: [gmx-users] trjconv behaving differently in 3.3.3 vs previous
> versions
>
> rob yang wrote:
>> Hi list,
>> I have a system solvated in dodecahedron box. To visualize it, I used:
>> trjconv -f system.gro -s system.gro -o visual.pdb -ur compact -pbc who
rob yang wrote:
Hi list,
I have a system solvated in dodecahedron box. To visualize it, I used:
trjconv -f system.gro -s system.gro -o visual.pdb -ur compact -pbc whole
Version 3.3.3 gave me a cubic box with broken molecules while the previous
versions gave me the right visualization on the same
Hi list,
I have a system solvated in dodecahedron box. To visualize it, I used:
trjconv -f system.gro -s system.gro -o visual.pdb -ur compact -pbc whole
Version 3.3.3 gave me a cubic box with broken molecules while the previous
versions gave me the right visualization on the same system.gro
Does
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