[gmx-users] DNA strands are separated

Peter Stern peter.stern at weizmann.ac.il
Tue Apr 24 09:36:53 CEST 2018


This is probably just a periodic boundary issue.  Use gmx trjconv with the -pbc nojump option to get both strands of dna in the same box.


-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> On Behalf Of spss4 at iacs.res.in
Sent: Tuesday, April 24, 2018 9:23 AM
To: gmx-users at gromacs.org
Subject: [gmx-users] DNA strands are separated

Hii all
I am trying to do DNA simulation in water. I have done 200ns mdrun for that. When I am trying to see the snapshot of different frames in VMD, it shows that DNA strands are separated and one strand is out of the box. So I couldn't get the picture of different frames with actual solvent orientation around the DNA. How to solve this problem?

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