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

[yunshi11 .]

On Sat, Feb 28, 2015 at 3:03 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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.
>
>
I did try that, and other combinations of -pbc and -ur options. Sorry that
I should have been more specific:

My system is a homo dimer of protein, each with two ligands (cofactor +
inhibitor) bound symmetrically. Some trjconv options can put the dimer
protein together, but the two ligands of the second monomer are always in
the other periodic boxes.

I am processing the trajectory after removal of solvents.




> -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
>
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