[gmx-users] Re: trjconv center problem

[Justin Lemkul]

On 4/19/13 4:37 PM, Brad Van Oosten wrote:
> Ahh, yes perhaps i was unclear.  The output file also has the same number of
> steps.
>
>
> Checking file md50_centered.xtc
> Reading frame       0 time    0.000
> # Atoms  27392
> Precision 0.001 (nm)
> Last frame      50000 time 100000.000
>
>
> Item        #frames Timestep (ps)
> Step         50001    2
> Time         50001    2
> Lambda           0
> Coords       50001    2
> Velocities       0
> Forces           0
> Box          50001    2
>
> The simulation is of a pure lipid bilayer, so the result of the centering
> option is that 99.9% of output frames have the lipid tales centered in the
> box while the 0.1% of frames seem not to be centered with the water at the
> center of the box.
>

This is not an issue of skipping frames at all, then.  It is an issue of your 
perception of "center," one that has been discussed many times on this list. 
This often happens with systems of lipids, multimeric proteins, or 
receptor-ligand complexes.  The "center" of a system is the geometric center, so 
two molecules together at the visual center of the box and two molecules on 
opposite "sides" of the box are both considered "centered" since the geometric 
center of the group coincides with the geometric center of the box.  Several 
iterations of trjconv (including -pbc or -fit options, in separate steps) may be 
necessary to achieve the desired outcome.

http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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