[gmx-users] gmx trjconv -pbc doesn't work

[Justin Lemkul]

On 7/9/18 10:20 AM, Chenlin Lu wrote:
> Hello all,
>
>
> Some of my trajectories has pbc problems. The substrate diffuses out of the pbc box. And I am trying to fix it using gromacs command gmx trjconv -f {}.xtc -s {}.tpr -o {}_nopbc.xtc  -pbc nojump. But the fixed trajectories still have same problems when I check them in VMD. I caculted the gyrations which show there are no significant changes for those fixed trajectoies. Is it because the presentation problem of VMD or gromacs pbc treatments. Any advice? (gromacs pbc treatment and VMD presentaion). Thanks in advance.

Most systems require multiple iterations of trjconv, starting with 
making molecules whole, then removing jumps, then perhaps other 
centering or re-wrapping operations. See 
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions#Suggested_trjconv_workflow

Without more information about what's in your system, what you tried, 
and what the actual outcome was, it's hard to suggest additional steps 
to take, but the link above should be a starting point.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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jalemkul at vt.edu | (540) 231-3129
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