Re: [AMBER] TUTORIAL A7 Replica Exchange Simulations with AMBER 10

From: Ross Walker <>
Date: Mon, 28 Jun 2010 11:36:43 -0700

Hi George,

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> The first one is related to Section 6 of the tutorial (REMD
> Simulations). Are these actual production simulations or one would need
> to run them for longer?

You'd probably need to run these longer. The key with any of these type of
simulations is that the longer you can run the better. Typically you should
always check for convergence. By, for example plotting convergence of the
property of interest against the cumulative number of points you include.
The example here would be to start with say 1ns and calculate the binding.
Then do 1.1ns, 1.2ns, 1.3ns etc and plot the binding energy as a point on a
binding energy vs cumulative trajectory length plot. This will show you what
the convergence looks like so you can make a coherent argument about whether
you need to simulate longer or not.
> The second question is only indirectly related. In the case that one
> would like to run REMD on a receptor/ligand complex, would there be any
> specific chirality restraints on the ligand different to those applied
> on the protein backbone?

This really depends on what the receptor / ligand look like. The issue is
that you are using artificially high temperatures which can cause certain
structures to be sampled that would not normally be accessible to the
system. The standard example if inversion of the backbone chirality. It is
certainly possible to see it in ligands as well depending on what their
structure is. The only real approach you can take here is to look carefully
at the structures and/or the results you obtain use chemical intuition to

Good luck,

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | |

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Received on Mon Jun 28 2010 - 12:00:04 PDT
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