[gmx-users] gromacs.org_gmx-users Digest, Vol 142, Issue 24

[Mark Abraham]

Hi,

As that page says, part of the issue is that different people need and want
different things, so there is not one magic recipe we can give, nor for
someone to find in a search. For example, it does not make sense to use the
cluster stage if you are centering on a single-chain protein. So the
workflow there prompts you to make that decision!

The centering options are described in trjconv -h, which that page has
already encouraged you to read. ;-)

If you want a chef to cook exactly the dinner you want to eat, you're going
to have to know a little about food and cooking! ;-)

Mark

On Fri, 5 Feb 2016 10:47 Timofey Tyugashev <tyugashev at niboch.nsc.ru> wrote:

>
> > Message: 4
> > Date: Thu, 4 Feb 2016 07:51:27 -0500
> > From: Justin Lemkul<jalemkul at vt.edu>
> > To:gmx-users at gromacs.org
> > Subject: Re: [gmx-users] trjconv options?
> > Message-ID:<56B3494F.4070703 at vt.edu>
> > Content-Type: text/plain; charset=windows-1252; format=flowed
> >
> >
> >
> > On 2/4/16 4:27 AM, Timofey Tyugashev wrote:
> >> >
> >> >
> >>> >>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>
> >>> >>Content-Type: text/plain; charset=windows-1252; format=flowed
> >>> >>
> >>> >>
> >>> >>
> >>> >>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?
> > Complex systems require complex operations.  Start with
> >
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow
> > because that order of operations generally works well.  Then see posts
> in the
> > archive, because this comes up frequently.  Typically, after making
> molecules
> > whole and removing jumps, you can center on a custom index group that
> defines
> > some useful center.  Then you can do whatever fitting you like.
> I've already looked at this page and it's not very helpful due to it's
> vague wording, so I guess trial and error is the only suitable way to
> get results. Due to the unstructured nature of mailing lists it's very
> hard to find relevant previous discussions. Probably that's why the
> topic comes up so frequently.
> Anyway, thank you for your suggestions.
> In your answer you suggest to go whole-jump-center route an the linked
> page says whole-cluster-jump-center. What is the difference between them?
> How is centering done? Define a new group, like one aminoacid in the
> middle of a protein, use '-center' on it and it'll be put in the
> designated position in box (specified by '-boxcenter')?
> --
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