Re: [AMBER] Imaging issue in DNA - cpptraj

From: Gustaf Olsson <gustaf.olsson.lnu.se>
Date: Wed, 2 Dec 2020 08:12:38 +0000

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 (https://amberhub.chpc.utah.edu/autoimage/), 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 <bo17resch11006.iith.ac.in<mailto:bo17resch11006.iith.ac.in>> 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 trajin.nc
autoimage
center :1-16 origin
image origin center familiar
center :1-32 origin
image origin center familiar
trajout reimage.nc
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

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*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 - 00:30:02 PST