[gmx-users] trjconv - two chains are separated

[Peter Stern]

I have also encountered this problem and was able to solve it using the tpr file generated before running editconf as the input to trjconv (with -pbc no jump).

Peter

Sent from my iPad

> On 3 בפבר׳ 2016, at 4:51, Catarina A. Carvalheda dos Santos <c.a.c.dossantos at dundee.ac.uk> wrote:
> 
> Hi there,
> 
> I had similar problems in the past. You'll have to play with trjconv and
> find the best combination of different flags to solve the visualization
> problem.
> 
> You can start by trying out this workflow for example:
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
> 
> Hope this helps.
> 
> Good luck!
> 
> 
> 
> On 3 February 2016 at 06:15, Trayder Thomas <trayder.thomas at monash.edu>
> wrote:
> 
>> For "-pbc nojump" to work, you need to make sure they are together (as you
>> want) in the first frame of your input trajectory.
>> 
>> The most reliable way to do this is by centering the trajectory on a
>> residue at the interface between the two chains (using a custom index
>> group).
>> 
>> I've also heard some people have had luck with "-pbc cluster"
>> 
>> You can then run "-pbc nojump" on the centered (or clustered) trajectory.
>> 
>> -Trayder
>> 
>> 
>> 
>> 
>>> On Wed, Feb 3, 2016 at 9:37 AM, Yunlong Liu <yliu120 at jh.edu> wrote:
>>> 
>>> Hi Gromacs Users,
>>> 
>>> I used "gmx trjconv" (Gromacs 5.0.4) to remove the pbc of my
>> trajectories.
>>> My protein has two chains (A and B) and they closely bind to each other.
>>> after running trjconv with "-pbc nojump", two chains are greatly
>> separated
>>> by a certain distance. It is mostly likely that the pbc is not
>> successfully
>>> removed and the program takes a chain from one unit cell and another from
>>> another unit cell.
>>> 
>>> Does anybody have any idea to solve the problem?
>>> 
>>> Best
>>> Yunlong
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> 
> 
> 
> -- 
> Catarina A. Carvalheda
> 
> PhD Student
> Computational Biology Division
> SLS & SSE
> University of Dundee
> DD1 5EH, Dundee, Scotland, UK
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