[gmx-users] trjconv options?

Justin Lemkul jalemkul at vt.edu
Thu Feb 4 13:51:40 CET 2016

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 
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.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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