AMBER Archive (2009)

Subject: Re: [AMBER] rmsd

From: Thomas Cheatham (tec3_at_utah.edu)
Date: Sat Nov 21 2009 - 15:44:41 CST

> I need help understanding an RMSd plot.
> after a dynamics run i use the following ptraj scripts

No one has responded yet, but as I look at the plots I too am confused...

(1) The plots seem too smooth.
(2) The RMSd is extremely large for 1 step (however I have no idea what 1
step means).

RMSd fluctuations are just that, fluctuations. Normally these are within
thermally accessible ranges of ~1-2 angstroms, depending on the system.

The large jumps suggest to me that there could be an imaging problem...
However your input shows IWRAP=1.

When you did the subsequent (second) ptraj step, did you start with a
prmtop that had no water? The previous step stripped it; the program has
no knowledge about the coordinates except what it expects from the prmop.
If you didn't run the second step with a prmtop without water, let me know
so we can debug...

-- tec3

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