AMBER Archive (2008)

Subject: RE: AMBER: using "EP" for dummy atom

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Nov 06 2008 - 20:05:22 CST

Hi Ashish,

 

You can simply create your own atom type (in a frcmod file and corresponding
residue template defining this atom's type / charge etc. See the first
advanced tutorial for an idea of how to do this if you don't already know.
Then in the frcmod file you just set the mass to zero.

 

You will of course need to modify the code in some way so that it knows how
to deal with this zero mass particle since otherwise as soon as you take a
time step there will be a division by zero when calculating the acceleration
of this particle and things will break.

 

Good luck,

Ross

 

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Ashish Sangwai
Sent: Thursday, November 06, 2008 5:24 PM
To: amber_at_scripps.edu
Subject: AMBER: using "EP" for dummy atom

 

Hello all,

I am trying to simulate a solute having a site with only force center and no
mass. My solvent is TIP4P water.

Which atom type should I assign to my zero mass site? I guess I can not
assign "EP" because its already taken by TIP4P water.

I do not want to give this site any mass as much as possible. Any help is
much appreciated.

Thank you very much for your help.

- Ashish Sangwai

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