RE: [gmx-users] trjconv behaving differently in 3.3.3 vs previous versions

: [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 whole Version 3.3.3 gave me a cubic box with broken

Re: [gmx-users] trjconv behaving differently in 3.3.3 vs previous versions

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 in 3.3.3 vs

RE: [gmx-users] trjconv behaving differently in 3.3.3 vs previous versions

@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

Re: [gmx-users] trjconv behaving differently in 3.3.3 vs previous versions

: [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

RE: [gmx-users] trjconv behaving differently in 3.3.3 vs previous versions

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

[gmx-users] trjconv behaving differently in 3.3.3 vs previous versions

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

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 whole Version 3.3.3 gave me a cubic box with broken molecules while the previous versions gave me the right visualization on the