AMBER: RE: Asking for help

From: Ross Walker <>
Date: Mon, 10 Sep 2007 16:31:24 -0700

Hi Lingyun,
I am happy to answer your questions but in future can I request that you
post queries via the amber mailing list ( - see for details on how to sign up. By posting queries
to this list you'll often get answers more quickly and more importantly the
questions and answers end up in an archive
( where other users can search them.
The question regarding heating your system vs hot starting it at 300 K
really depends on how stable a system you have to begin with and this
depends on how good your initial structure looks. If you have a well
equilibrated solution phase structure then you can probably get away with
starting it at 300 K. However, if you have a crystal structure, that you
have just solvated, by hot starting at 300 K you may find that there are
stability problems due to bad steric clashes etc. Or if the simulation
doesn't show any initial problems you may have ended up giving the system an
unrealistic perturbation. The problems are a function of crystal structures
being low resolution and/or solid state structures and the fact that leap
has to add a number of solvent molecules that can clash with protein atoms
etc. Thus a way around this problem is to heat the system up slowly in what
is a more controlled fashion so that the system has a chance to relax away
from what is an initial high energy state.
Note, for small systems, like small peptides in water, and also for implicit
solvent systems it is possible to just start them at 300 K without any
problems but it is so easy to heat a system slowly that you might as well do
it to be on the safe side.
In answer to your question about restraining the protein during initial
heating in explicit solvent this is not normally necessary. It is included
in the tutorial because in some cases, especially with homology modelled
starting structures, or structures where missing residues have been added
etc, it is necessary to use restraints initially to obtain a stable
simulation. Thus this essentially represents a worst case scenario.
The question of how long a simulation is suitable is extremely difficult to
answer and is largely a function of what you are looking to observe.
Typically the larger a system the more sampling you will need to do. Rule of
thumb these days is that simulations should typically be on the nanosecond
timescale at least but certainly one could write several Ph.D.s on this
question. For the heating stage it just needs to be slow enough that your
system isn't badly perturbed by this. Something on the order of 100ps or so
is probably reasonable for most systems.
With regards to different simulations giving different results yes indeed
this is true. Simulations started from different initial structures, started
with different random seeds, or even just run on different numbers of
processors will follow different trajectories. But none is more right than
any of the others. The issue is one of ensemble averaged behaviour. I.e. if
you have run long enough sampling then all of the simulations should
converge to the same result. If they do not then you may be sampling
behviour that is a function of your starting conditions rather than a aspect
of the system you are simulating.
Good luck...

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| <> | PGP Key
available on request |

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From: Wang ling yun []
Sent: Thursday, August 30, 2007 19:11
Subject: Asking for help

Hi Professor :

    I am a new amber user , may I ask you some questions ?

    In a md simulation , is nescessary heating the system ? May I run a
simulation at 300K directly ? What's the role of heating ?

    If I do a protein simulation in explict model, is it necessary to
constrain the protein or not ? How long the simulation is suitable ? And do
the different simulations make different results ?


Thank you for help !

Lingyun Wang

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Received on Wed Sep 12 2007 - 06:07:35 PDT
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