Re: [AMBER] High RMSD values due to use of iwrap

From: David A Case <>
Date: Fri, 8 Jan 2016 09:07:59 -0500

On Fri, Jan 08, 2016, richa anand wrote:

> I performed the MD simulation of 50 ns for RNA-Protein complex with iwrap =
> 0. But after 45 ns simulation got stuck. The error was: it could not
> identify the co-ordinates. To run whole simulation then I used iwrap = 1.
> It run for 50 ns, but when I measured RMSD values for C-alpha pf protein it
> went to 14-20 A.

It is possible using iwrap=1 can do odd things when you have more than one
macromolecule. Cpptraj gives you much more control over how the imaging is
done. I suggest that you make sure to use netCDF restart and trajectory files
(set ioutfm=1 and ntxo=2); then you don't have to concern yourself much with
the value of iwrap.

> I am confused that when I use iwrap why I get high values of RMSD, while
> the same input file to calculate RMSD gives low values of RMSD without
> using iwrap (i.e. iwrap = 0). But using iwrap = 0 simulation get stuck
> after 45 ns.
> Please suggest me how to get right values of RMSD. I used 'image' command
> during RMSD calculation.

Here, and in general, we need details of *exactly* what commands you used.
In almost all cases, using the "autoimage" command in cpptraj does the right
thing. Use that before the RMS command.


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Received on Fri Jan 08 2016 - 06:30:06 PST
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