AMBER Archive (2006)

Subject: AMBER: center molecule using iwrap=1?

From: Gustavo Seabra (
Date: Thu Jul 13 2006 - 13:21:17 CDT

Hi All,

I have a system of a small peptide in explicit water.

I know that, using ptraj, I can put the peptide inthe center of the
box and wrap all waters around it, so as to create a new crd file with
my molecule always in the center of the box and wrapping the waters
around it.

I wonder if something like it is possible by using iwrap=1 instead. I
mean, define it to wrap the molecules, (iwrap=1) AND keep the peptide
in the center od the box. Is that possible? How?

(I'm worried that just with iwrap=1 alone the peptide will be allowed
to drift inside the box. Although it has no effect on the dynamics, it
will change the analysis I want to do later.)

Thanks a lot!

Gustavo Seabra                                    Postdoctoral Associate
Quantum Theory Project                             University of Florida
Registered Linux user number 381680
Say NO! to software patents:
If at first you don't succeed...
                              ...skydiving is not for you.
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