Re: [AMBER] Strange RMSD tower appearing in simulation

From: Dr. Anselm Horn <>
Date: Wed, 9 Sep 2020 10:12:56 +0200

Following the call to chime in:

>From the shape of the RMSD plot, I'm pretty sure that this indicates an
imaging (or wrapping) problem originating from the use of iwrap=1. I
have seen many similar graphs in multimeric protein systems in my own
raw MD runs (, but also in published work).
Visual inspection of the simulation runs yielded an instantaneous "jump"
of one or more protein chains from one trajectory frame to the other.

Dave's analysis of the problem and David's advice to use the "unwrap"
option in cpptraj worked for me in all the cases.

Note, however, that you may have to use your original water-containing,
not-yet rmsd-fit trajectory for that procedure. But be sure to do the
deletion of solvent molecules *prior* to the unwrapping; otherwise you'd
create an unnecessary computational burden for your machine.



On 09/08/2020 08:23 PM, David A Case wrote:
> On Tue, Sep 08, 2020, Dave Cerutti wrote:
>> Yes, this looks like an imaging problem--if you have iwrap = 1 in your
>> &cntrl, the homoDIMERIC protein is two molecules, so each will be re-imaged
>> separately.
> Everyone wants to chime in on this one!
> It would be good to know if you are indeed using iwrap=1. If so, you
> see a reaoson to avoid that in the future.
> You *should* be able to undo the wrapping in cpptraj, and get a proper
> RMS vs. time plot, without having to re-run any of the simulation.
> Check out the "unwrap" option in cpptraj.
> [This all assumes that this is indeed a wrapping problem -- as Carlos
> suggests, visualization is your friend here.]
> ....dac
> _______________________________________________
> AMBER mailing list

AMBER mailing list
Received on Wed Sep 09 2020 - 01:30:02 PDT
Custom Search