AMBER Archive (2004)

Subject: Re: AMBER: question about image

From: pengyo_at_UMDNJ.EDU
Date: Fri Apr 02 2004 - 21:35:06 CST

Dear Thomas,
Thanks a lot for your help.
Could you please tell me How I can find out if the solute drifts over time
during MD? In what situation imaging is needed?

Youyi

Quoting "Thomas E. Cheatham, III" <cheatham_at_chpc.utah.edu>:

>
> > I have a general question about imaging. After MD simulation in PBC,
> what
> > kind of problems will be generated if no ptraj/image post-processing?
> What
> > difference will be made before and after imaging? I compared RMSD of
> > trajectory files before and after, and it looks no difference. Does
> imaging
> > affect the fitting and averaging of structures? I don't really
> understand
> > what imaging does and what kind of effects it will have.
>
> PBC implies that the system is periodic and also that our complete
> system
> represents 1 unit cell worth of data. However, as the system is
> periodic,
> our particles can be in any of periodic units i.e. they can drift over
> time out of the primary unit cell into adjacent. This will happen
> naturally over time in MD simulation unless IWRAP=1. This leads to
> the system *appearing* to blow up, when in fact if it is imaged to
> put all the outside atoms back into the primary unit cell, things
> look again normal.
>
> i.e. this...
>
> ----------------
> | | | |
> | | | |
> ----------------
> | |1 | |
> | | xx2| |
> ----------------
> | | | |
> | | | |
> ----------------
>
> ...is equivalent to...
>
> ----------------
> | | | |
> | | | |
> ----------------
> | |1 | |
> | | x | |
> ----------------
> | | | |
> | | x | 2|
> ----------------
>
> If your analysis program is set up to correctly image distances, angles,
> etc, there should be no difference before and after imaging... However,
> if
> it is NOT, the results will not be equivalent. For example, consider
> the
> distance between 1+2 above which will be different in the two cases
> unless
> the imaging is performed.
>
> Molecules are typically imaged together; if you have a one molecule
> psolute, then RMSd on this will not change before and after imaging. If
> you have two molecules, the RMSd may change if the molecules end up in
> different cells within the periodic lattice...
>
> So, yes, in general, imaging may affect RMSd estimations and averaging
> of
> structures as both of these commands (in carnal or ptraj) do not image.
> [The distance commands in general do image, but not rms or average]
>
> (p.s. if your trajectory file is unchanged before and after imaging then
> either it didn't image OR no particles moved out of the primary unit
> cell
> OR whatever you are RMS fitting never separated into multiple unit
> cells)
>
> 

-- 

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu