Hmm. I am getting the desired output now, at least as far as the pulled
atoms are concerned, they are all close to the bilayer center (was not so in
a free simulation), and therefore my suspicion is that the code is working.
Just to re-iterate, the atoms to be pulled to the bilayer center were
Dear Chris,
Thank you for the code. I did check out pull_pbcatomN, and thank you for the
heads up that it is a global index. I used a central atom in the box for
each of the two groups as pull_pbcatom.
After using the code below with a rate constant of ~ 5500 for about 100 ps,
I realized that
Maria,
I highly doubt that you are correct. If you want more help, please
copy and paste your commands and some relevant output back to the list.
Chris.
--original message --
Message: 4
Date: Wed, 8 Sep 2010 15:07:15 +0200
From: maria goranovic mariagorano...@gmail.com
Subject: Re:
maria goranovic wrote:
I want to restrain certain atoms of my simulation to the plane
perpendicular to the bilayer normal, and at the bilayer center. Can
someone please provide a quick guide on how to do this? I read the
pull-code options, but restraining to a plane did not seem possible?
The manual does discuss restraining to a plane, but this must be the plane
in which the atom is already present.
[ position_restraints ]
; ai functfc
...
3 1 1000 0 0
How about restraining the atom to some other plane? For example, how about
restraining a phosphate group initially
Maria, try this. There actually is a lot of this on the mailing list,
so I suggest checking it a little deeper for your next querry, or at
least outlining how you looked and what you found so that it is clear
you have tried.
Also, read about pull_pbcatomN and think carefully about how you
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