[AMBER] missing AMBER features for simulating surfaces and linear assemblies

From: Andrew Jewett <jewett.ai.gmail.com>
Date: Mon, 7 Mar 2011 02:18:31 -0800

A couple of us in the Shea group at UCSB have begun projects in AMBER,
and abandoned them, using other software instead.  Our recent work
requires simulating large (infinite) surfaces and polymers immersed in
solvent.  AMBER lacks a few small features that have prevented us from
tackling these kinds of simulations. If the amber community is considering
adding new features to AMBER, then please consider the following:

i) The ability for a covalent bond to cross the periodic box boundary.
ii) The ability to allow pressure rescaling in only the Z direction.
   (while preventing rescaling in the XY directions, or visa versa).
   This is useful when equilibrating the solvent near an infinite surface.
iii) NPT simulations do not work when constraining large solutes,
fibers or surfaces.
 a) Harmonic restraint anchor points are not fixed during NPT simulations,
   but are scaled.  It would be useful to make this optional
   (both for belly and harmonic restraints).
 b) Arguably, constraints cause the virial to be calculated incorrectly.
  This can force the box to expand to a huge size.
   (See attached figure. I will post another message on this topic.)

Recently, in the AMBER mailing lists, David Case also expressed
concern that the "unit cell dimensions must be more than twice the
non-bonded cutoff, so small unit cells are not feasible".
I just wanted to reply to this point. For us, this has not yet been a problem.
(All of our systems were larger than 24 Angstroms in every dimension.)

For reference, here are the projects in our group in the last few
years which we tried and failed to simulate using AMBER:
1) Simulating the interaction between ice and water
2) Simulating the interaction of an enzyme with cellulose
3) Simulating the interaction of a small peptide with a hydrophobic surface
4) Simulating an infinite helix of polyalanine (I think..)

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Received on Mon Mar 07 2011 - 02:30:03 PST
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