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
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
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