Date: Wed, 2 Dec 2020 12:47:22 +0530
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
-- *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* -- Disclaimer:- The information contained in this electronic message and any attachments to this message are intended for the exclusive use of the addressee(s) and may contain proprietary, confidential or privileged information. If you are not the intended recipient, you should not disseminate, distribute or copy this email. Please notify the sender immediately and destroy all copies of this message and any attachments. The views expressed in this E-mail message (including the enclosure/(s) or attachment/(s) if any) are those of the individual sender, except where the sender expressly, and with authority, states them to be the views of IIT Hyderabad. Before opening any mail and attachments please check them for viruses, malware, and the sender email address is indeed from IITH domain. IITH does not accept any liability for malware infected mails.
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