AMBER Archive (2009)

Subject: Re: [AMBER] rmsd

From: Taufik Al-Sarraj (
Date: Mon Nov 23 2009 - 13:24:49 CST

Hi Thomas,
The plots are smooth because i plotted the data using a smooth line,
using xmgrace the plots are not smooth. 1 step means 5,000 steps/after
10ps of dynamics.

i don't think i changed anything in the prmtop file. i only strip water
from the .mdcrd files and then use the rms command on the *.mdcrd files
that have the water molecules striped and are imaged (using image familiar).

i run ptraj *.prmtop (file with water) rms.trajin

trajin shorttwoMD1nowat.mdcrd <--(water is stripped)
reference shorttwoheat1.rst
rms reference mass out lin.dat ':1' time 0.2
rms reference out SUR.dat ':2' time 0.2
rms reference out APT.dat ':3' time 0.2
rms reference out DNAca.dat ':4-22@%CA' time 0.2
rms reference mass out DNA.dat ':4-22' time 0.2
rms reference mass out olig1.dat ':23-74' time 0.2
rms reference mass out olig2.dat ':75-126' time 0.2
rms reference out Naion.dat ':127-145' time 0.2

Thomas Cheatham wrote:
>> 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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