[gmx-users] DNA strands are separated

[spss4 at iacs.res.in]

  ----- Message from Peter Stern <peter.stern at weizmann.ac.il> ---------
    Date: Tue, 24 Apr 2018 07:36:48 +0000
    From: Peter Stern <peter.stern at weizmann.ac.il>
Reply-To: gmx-users at gromacs.org
Subject: Re: [gmx-users] DNA strands are separated
      To: "'gmx-users at gromacs.org'" <gmx-users at gromacs.org>

> Hi,
>
> 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.
>
> Regards,
> Peter
> Thank you Peter for replying. Actually I have tried this with -pbc
> nojump but its not working for my case.
> -----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?
>
> Thanks
> sunipa
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----- End message from Peter Stern <peter.stern at weizmann.ac.il> -----