AMBER Archive (2004)

Subject: Re: AMBER: Ptraj data

From: Elijah Gregory (ejgregory_at_gmail.com)
Date: Tue Sep 21 2004 - 17:04:45 CDT

If during your simulation you only dumped output to a file every 50ps
then you will not be able to get RMSd information every 1ps. How can
the program guess what the atomic positions are each picosecond if you
only save these positions every 50 picoseconds? In other words, the
program only has information about the atomic positions at 50ps,
100ps, 150ps...etc. and it cannot guess what happened in between these
times.

If you use the 'time 50' option in the RMSd command then you will get
RMSd values at 0ps, 2500ps, 5000ps, 7500ps... etc. But unless you
saved your data during the simulation each and every picosecond then
there is no way you can get the RMSd values at these times unless you
do some interpolation which will almost certainly fail since the MD
trajectories are not exactly "well-behaved" functions.

~Elijah Gregory

On Tue, 21 Sep 2004 12:59:58 -0600 (Mountain Daylight Time), Thomas E.
Cheatham, III <cheatham_at_chpc.utah.edu> wrote:
>
> > I have been using ptraj to get RMSd. However, when I get the data it
> > places the number of frames (and not the time in picoseconds) on the
> > x-axis. That is, I have 1000 frames with each at 2500 steps (50 ps).
>
> If I understand you correctly, you want the data to be "ps" vs. time
> rather than "frame #" vs. time. This can be accomplished via the time
> keyword to RMS as you've used. It is possible that this is not being
> parsed correctly? Also, I think you want the time to be 50.0 not 0.5; try
> moving the time keyword and value before the mask...
>
> > rms first out N25D3_data1 :1 time 0.5
>
> rms first out N25D3_data1 time 50.0 :1
>
> (Also, I am not clear exactly how much information you will obtain from
> doing the best fit RMSd of a single residue; I guess this might give
> insight into flips to different conformations?)
>
> Good luck and let us know if you have further questions.
>
> --tom
>
>
>
>
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