[gmx-users] Confuse about trjconv tool

[Justin Lemkul]

On 9/21/13 10:28 PM, Caizk wrote:
> Dear users,
>
> I was following Justin's tutorial and in the analysis step trjconv was used to account for any periodicity in the system and then analyses were conducted with the so-called "corrected" trajectory file.
>

The first thing that is important to note is that the use of the word 
"corrected" does not imply that the original trajectory is in any way 
"incorrect."  It's just a colloquialism because the trjconv output is easier to 
visualize and thus seems more "correct" when pulled up in the visualization 
software of choice, rather than having a bunch of "broken" molecules and weird 
lines drawn all over the place.

> The first question is: does it means that particles might diffuse though one side of the box and doesn't get into the box from the opposite side?
>

No, that is not the case.  Periodicity is always correctly maintained during the 
run.

> If not, why does trjconv have  to be used? If so, why could't gromacs maintain the periodicity of all 
particles' coordinates in the production MD?
>

It is a waste of CPU cycles for mdrun to try to "fix" something during the run 
that doesn't matter at all to the physics going on.  Using trjconv is not 
compulsory for all processes, but it is important for visualization and certain 
analyses that require intact coordinates (like RMSD).

> Finally, Is it necessary to use trjconv to currect the trajectory file every time before you conduct any analysis?
>

As above, it depends on the analysis.  Most tools handle PBC elegantly.  Some don't.

-Justin

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

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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