From: dhirajks_at_gmail.com
Date: Wed Oct 05 2016 - 11:03:41 CDT
Sorry. I should have labeled it. Y axis is time in picosecond and x axis is rmsd in Angstrom.
Dhiraj
Sent from my iPhone
> On Oct 5, 2016, at 10:55 AM, Pardis Tabaee <pardis.tabaee.d_at_hotmail.co.uk> wrote:
>
> Hi,
>
>
> What's on the y axis?
>
>
> Regards,
>
>
> P
>
>
> From: owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of Dhiraj Srivastava <dhirajks_at_gmail.com>
> Sent: 04 October 2016 22:07
> To: namd-l_at_ks.uiuc.edu
> Subject: namd-l: question regarding rmsd
>
> Hi
> I am trying to do MD simulation on a protein with and without ligand. when I did rmsd plot, I found that apo protein is behaving fine (red) but ligand bound form (black) is taking relatively longer time to equilibrate and showing quite a bit of fluctuation in rmsd. is the fluctuation in rmsd value for ligand bound protein is acceptable or is there anything wrong? How can I fix it?
>
> thanks
> Dhiraj
>
>
>
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