Hello George,
Two possible reasons for the behavior you observe are:
1. You started with a crystal structure of your protein and the structure relaxes in solution. This happens for some multimeric proteins for example. In this case, the long term rmsd fluctuates around a steady average value. We are investigated specific cases of this in my laboratory - work in progress. Your equilibration run appears to show this behavior.
2. You have an intrinsically flexible protein and there a continual fluctuations in the structure as the simulation progresses. One example of this case is an antibody (see Brandt et al, Biophysical J. 99, 905-913(2010)). An antibody (150 kDa)is not a small protein and in order to characterize such a structure we performed block simulations with more than an aggregate of 320 ns in length. You do not state what your protein is, but it must be small, given the time scales you are using. An example of a small protein that shows discernible fluctuations is mouse ubiquitin (has 20% of its residues in a long flexible tail). Some of this work is described in a publication we are about to submit.
I assume you have taken out the motion of the center of mass in computing your rmsd.
Jason's suggestion regarding the visualization of the trajectory is an excellent idea.
Cheers, Sergio
Sergio Aragon
Professor of Chemistry
SFSU
-----Original Message-----
From: George Tzotzos [mailto:gtzotzos.me.com]
Sent: Friday, January 07, 2011 10:33 AM
To: AMBER Mailing List
Subject: [AMBER] Drifting RMSD
Hi everybody,
I'm sure that some of you must have made a similar observation.
Following equilibration, and during the production run the backbone rmsd of the protein is drifting. I'm attaching two snapshots for easy reference. The equilibration run was over 6ns and the production run over 14ns. The md.in files are identical.
Any ideas regarding this behaviour?
Many thanks
George
EQUILIBRATION: md.in
heat 3ogn-3og
&cntrl
imin=0,irest=1,ntx=5,
nstlim=1000000,dt=0.002,
ntc=2,ntf=2,
cut=8.0, ntb=2, ntp=1, taup=2.0,
ntpr=1000, ntwx=1000,
ntt=3, gamma_ln=2.0, ig=-1,
temp0=300.0,
/
================
PRODUCTION: md.in
heat 3ogn-3og
&cntrl
imin=0,irest=1,ntx=5,
nstlim=1000000,dt=0.002,
ntc=2,ntf=2,
cut=8.0, ntb=2, ntp=1, taup=2.0,
ntpr=5000, ntwx=5000,
ntt=3, gamma_ln=2.0, ig=-1,
temp0=300.0,
/
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Received on Fri Jan 07 2011 - 11:00:03 PST
