Re: Accelerated MD with transmembrane protein

From: Jeff Wereszczynski (
Date: Fri Apr 11 2014 - 07:19:20 CDT

Hi Kevin,

Which version of NAMD are you using? I don't think aMD was working on the
GPUs for the nonbonded terms in version 2.9, but it looks like they've
fixed it in the nightly builds (I haven't tried it though).

Also, are you turning on your aMD forces at 300K? You may want to try
heating your system with the aMD forces on, or even minimizing then heating
your system with the aMD forces on.


Jeff Wereszczynski
Assistant Professor of Physics
Illinois Institute of Technology

On Fri, Apr 11, 2014 at 3:27 AM, Felipe Merino <> wrote:

> Hi,
> The rules for defining the acceleration parameters that you cite were
> meant to be used with proteins primarily as far as i remember. Actually,
> they are more a rule of thumb than anything else. For systems with lipids
> the choice can a bit different as the dihedral energy per residue on a
> lipid is quite different than an aminoacid.
> Take a look at this paper, the define the parameters based directly on the
> dihedral energy Miao Y, Nichols SE, McCammon JA (2014). Physical Chemistry
> Chemical Physics 16(14):6398- 6406.
> Have in mind that for big systems the acceleration (dV) gets a bit too big
> and then in practice you cannot reweight the final distribution simply
> because you average gets dominated by conformations that you rarely sample
> (very high exp(dV*beta)
> Being that said, I never saw my aMD simulations fail with a constraint
> failure even with pretty huge acceleration (I even use it sometimes to
> remove gross error from initial models) which
> suggests that your systems have issues unrelated to the acceleration.
> Hope that helps
> Best
> Felipe
> On 04/10/2014 08:40 PM, Kevin Kastner wrote:
> Hello all! I am trying to use accelerated molecular dynamics on NAMD for
> a protein that is inside of a lipid bilayer and am having trouble.
> Previously, I had set up and run the simulation using the NAMD membrane
> tutorial and have gotten that to work (though I have converted it to use
> the amber force field instead of CHARMM). From other sources I have
> calculated the energies and alphas for each of the protein + system and the
> membrane to be the following:
> accelMDE = <dihedral energy from standard simulation> + 4 * (# of
> residues) + 40 * (# of POPC molecules)
> accelMDalpha = 1/5 * 4 * (# of residues) + 20 * (# of POPC molecules)
> accelMDTE = <total energy from standard simulation> - <dihedral energy
> from standard simulation> + 0.16 * (# of total atoms)
> accelMDTalpha = 0.16 * (# of total atoms)
> I have tried running with these new parameters both starting after the
> three preparation steps that need to be done with transmembrane systems
> (melting the lipid tails, then constraining the protein, and finally
> letting the whole system equilibrate) and also starting at the very
> beginning with the three steps using aMD, but the system crashes after a
> short while every time. Usually the error has to do with the SHAKE or
> RATTLE algorithms.
> Does anyone know anything else I need to do to get this to work? Do I
> need to reduce the size of the timesteps from 2fs to 1fs? Or do I need to
> do something else? Oh, I do not know if this makes a difference, but I am
> also trying to run this on GPUs, rather than CPUs. Is aMD not compatible
> with GPU-accelerated MD? I would appreciate any help that anyone can
> provide. Thank you!
> --
> - Kevin Kastner
> "For me, insanity is super sanity. The normal is psychotic. Normal means
> lack of imagination, lack of creativity." - Jean Dubuffet

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