Re: [AMBER] Issue in drug parameter

From: David A Case <>
Date: Sun, 1 Mar 2020 17:28:39 -0500

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.


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Received on Sun Mar 01 2020 - 14:30:02 PST
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