[gmx-users] the treatments of the periodic boundary condition

[Justin Lemkul]

On 7/10/16 11:55 PM, 15110700076 at fudan.edu.cn wrote:
>
>
> Hello everyone,
>       My several systems of  a protein-ligand complex were put into the dodecahedron box and were applied to 20ns runs. However, the ligands in these systems ran out of the boxes in the raw trajectories. After I treated these trajectories by "trjconv", the ligands and proteins could not come into the box at the same time. But the ligands were closed to the holes in waters where the proteins should be, it suggests that ligands should form H-bonds with proteins in some time points. How can I do to get the whole complex in the box, or the ligands may be distant from proteins in truth. My trajectory treatment commands are following:
> trjconv -f md_0-20ns.xtc  -s md_1.tpr -o md_0-20ns_nojump.xtc -pbc nojump -n system.ndx

You need to cluster and/or put molecules back in the box here.

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

-Justin

> trjconv -f md_0-20ns_nojump.xtc -s md_1.tpr -o md_0-20ns_nojump_fit.xtc -fit rot+trans -n system.ndx
> trjconv -f md_0-20ns_nojump_fit.xtc -s md_1.tpr -o md_every100ps.pdb -dt 100 -n system.ndx
>
>
> thank you!
>
>
>
> --
>
>
> Best wishes,
>
> ------------------------------------------------------------
>
> Qing Liu
>
> Fudan Univ.
>
> E-mail: 15110700076 at fudan.edu.cn
>

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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