[gmx-users] First frame already out of box, getting very large RMSD

[Justin Lemkul]

On 2/28/15 6:00 PM, yunshi11 . wrote:
> Dear all,
>
> I am running MD for a protein-ligand complex in a dodecahedron box and
> followed the "Suggested trjconv workflow" from
> http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
> .
>
> Now I wonder how to remove jumps (across periodic boxes) when the first
> frame (actually the .gro file from equilibration run) is already jumping
> across two (or more) boxes (according to visualization in VMD).
>
> I understand that this is just an visualizing artifact, but it seems to
> also affect other analyses such as calculations of RMSD along the
> trajectory. I got some impossible RMSD values like 1.5 nm, considering
> other replicate simulations give only ~0.3 nm.
>
> Any idea on how to fix this (the effect on RMSD calculations etc., not
> visualization)?
>

trjconv -center -pbc mol -ur compact usually solves all problems for such simple 
systems.  Center on the protein, everything else gets re-wrapped around it. 
More complex operations would be needed for protein complexes, membranes, etc. 
But proteins in water (with or without ligands) are generally straightforward.

-Justin

-- 
==================================================

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

==================================================