Re: [AMBER] Imaging issue in DNA - cpptraj

From: Dr. Anselm Horn <>
Date: Wed, 2 Dec 2020 10:23:56 +0100


just to add a comment:
If you used iwrap=1 in your simulation input, try to use the unwrap
command in cpptraj, expecially, if you are not interested in the solvent
molecules: strip off these first, the do the unwrap and omit the
(auto)image commands.

However, you may want to use a rms fit command to obtain a trajectory
better to visualize.



On 12/02/2020 09:12 AM, Gustaf Olsson wrote:
> Short of increasing the solvent buffer to avoid jumps, trying to play around with the masks for image/autoimage seems reasonable.
> See what happens if you autoimage with a mask defined. Either trying to center the entire DNA or as suggested (, try imaging using a small region of the DNA which should be close to the center of the box.
> Best regards
> // Gustaf
> On 2 Dec 2020, at 08:17, Satyaseelan C <<>> wrote:
> Dear Amber users,
> I am facing an imaging issue during the MD simulation of a
> DNA duplex. Due to this, the RMSD is shooting up and falls back during the
> middle of the simulation. I am observing this problem for 50ns during the
> simulation. I used autoimage option followed by image option as below:
> parm prmtop
> trajin
> autoimage
> center :1-16 origin
> image origin center familiar
> center :1-32 origin
> image origin center familiar
> trajout
> go
> When I don't apply any imaging, the DNA strands are separated and going out
> of the box in some frames. But, after performing imaging, the problem is
> not completely resolved. Here, a stretch of DNA strand is going away and
> causes distortions in the structure for 50ns. I have attached the
> corresponding snapshots.
> Please suggest any alternative options to overcome this issue.
> Thanks in advance
> Sathyaseelan
> --
> *Thanks & Regards*
> *C .Sathyaseelan *
> *PhD Research Scholar*
> *C/o Dr. Thenmalarchelvi Rathinavelan*
> *Molecular Biophysics Lab*
> *Dept. of Biotechnology*
> *Indian Institute of Technology (IIT)*
> *Kandi, Hyderabad, Telangana - 502285*
> *Ph.No 6383836804, 8300150807*
> --
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Received on Wed Dec 02 2020 - 01:30:02 PST
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