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

Timofey Tyugashev tyugashev at niboch.nsc.ru
Fri Feb 5 10:47:22 CET 2016

> 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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