[gmx-users] How to apply trjconv -nojump to a part of a system

[Emanuel Birru]

Thanks mate, I am trying it now :)


-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Trayder Thomas
Sent: Thursday, 11 July 2013 11:52 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] How to apply trjconv -nojump to a part of a system

VMD might do what you want with the PBC tools plugin (installed by default). http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/
unwrap being the equivalent of -nojump

Otherwise, couldn't you just view your 2 trajectories simultaneously, one with protein the other not?

-Trayder


On Wed, Jul 10, 2013 at 9:13 AM, Bin Liu <fdusuperstring at gmail.com> wrote:

> Hi All,
>
> For the convenience of visualization, I need to remove the jump of one 
> component (say a protein) of the system at the boundary. I don't need 
> to, or say I need not to remove the jump of the other components (say 
> a lipid bilayer), since otherwise the system will look falling apart. 
> I noticed I can cluster a part of a system, then output all the atoms 
> in the system in which only the part is clustered, and the other 
> components unchanged. Does GROMACS have similar function when *-nojump* is used?
>
> If this can not be accomplished directly, is there a way to circumvent it?
> I figured out a way, but haven't implemented it. I can plug the 
> coordinates of the protein treated with *-nojump* into the trajectory 
> of the whole system which is not treated with *-nojump*. It is kind of 
> substituting the coordinates of one component in one trajectory with 
> the coordinates of the same component in another trajectory. Is there 
> anyone aware of a tool or a script to do this job?
>
> Thank you very much.
>
> Regards
>
> Bin
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