[gmx-users] trjconv options?

[Timofey Tyugashev]

> Message: 2
> Date: Wed, 3 Feb 2016 07:37:42 -0500
> From: Justin Lemkul<jalemkul at vt.edu>
> To:gmx-users at gromacs.org
> Subject: Re: [gmx-users] trjconv options?
> Message-ID:<56B1F496.5090604 at vt.edu>
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> On 2/3/16 6:34 AM, Timofey Tyugashev wrote:
>> >Thank you for replies on my previous questions.
>> >And now I have another one dealing with trjconv.
>> >
>> >I have a simulation of  a three-chain protein/nucleic acid complex. Naturally,
>> >it gets broken in three separate strands by PBC.
>> >After trying several, I settled on using options '-pbc mol' with '-ur compact'
>> >which makes the complex look decent again and it looks like that does the job.
>> >But I'm worried about a possibility of something getting unrepaired by this
>> >option and getting unnoticed by me. What is the way to check for it?
> Any molecules that appear to fly away suddenly will be a pretty dead giveaway.
>
> In general, for multimeric complexes, you need to do a lot more work, e.g.
> centering on a single chain after making molecules whole and removing jumps.  If
> a simple -pbc mol -ur compact does the trick, probably nothing has actually
> crossed a periodic boundary yet.
>
>> >Also it keeps tumbling around the cell during the trajectory. It's annoying. Is
>> >there a way to pin down the cluster and stop it from rotating?
> This is what trjconv -fit is for.
>
> -Justin
Well, both vmd and pymol render .gro file (and trajectory files) with 
DNA strands and protein positioned in different corners of the box.
Also, editconf -pbc has no effect on .gro file with the broken complex. 
How it's supposed to behave?

So in this case I should at first run trjconv with '-pbc whole', make 
second run with '-pbc nojump', then make third run with '-pbc mol' to 
properly repair the trajectory?
I guess for -fit I should pick 'progressive' option?