I think that using iwrap=1 is what led to this, it made the ligand or
protein get imaged by itself when it got to the edge. Autoimage moves them
back together. This won't happen when iwrap=0, as Dave says.
On Sun, Mar 1, 2020, 5:28 PM David A Case <david.case.rutgers.edu> wrote:
> On Sun, Mar 01, 2020, SHAUNAK BADANI wrote:
> >
> >Thanks for your reply. I used autoimage and the drug is properly
> >surrounded by water molecules now. However, I am not able to clearly
> >understand the reason behind this behaviour as I used iwrap=1 during my
> >equilibration, under the assumption that this won't occur. Could you
> >suggest a plausible explanation?
>
> Not withoug more information. The problem with iwrap=1 is that it
> implements only the simplest form of imaging, and is much less "smart"
> than is autoimage. (Dan Roe has put in lots of effort to make autoimage
> work as well as it does. Even so, there are times when users have to
> use the "image" command itself, and select all the options by hand.)
>
> There is really no good reason (in my view) to even have the iwrap=1
> option anymore. It served a purpose a decade ago, and still (I admit)
> can be useful for very simple simulations. But I'm not the best person
> to answer your original question, since I never use that option myself.
>
> ....dac
>
>
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Received on Sun Mar 01 2020 - 15:00:03 PST
