Re: [AMBER] pbc problem

From: David A Case <>
Date: Thu, 24 Jul 2014 16:38:53 -0400

On Thu, Jul 24, 2014, Niloofar Nayebi wrote:
> I have introduced MoS2 to Amber and put heavy constraint on these atoms and
> try to relax a 12-mer peptide on it. When I used the periodic boundary
> condition in heating stage everything fell apart and peptide atoms started
> to replace Mo on the surface!! I turn the periodic boundary condition off
> and it is working!! I am using explicit solvation and here is the script I
> am using for heating:

There is not enough information given to figure out the source of the
problem. What does "everything fell apart" mean? Some comments:

> nstlim=2500000,
> ntpr=500,

Try setting nstlim=250 and ntpr=1. That may give you helpful information for

> constrains
> 1000.0

Set this to something like 10. What you have is way to strong to carry out MD
with a time step of 2 fs.

You might also use or cpptraj to examine the non-bonded interactions
between the surface atoms and the peptide. Visualization of the trajectories
might also provide some clues.


AMBER mailing list
Received on Thu Jul 24 2014 - 14:01:49 PDT
Custom Search