Re: Accelerated MD with transmembrane protein

From: Jeff Wereszczynski (
Date: Fri Apr 11 2014 - 11:50:20 CDT

According to the CVS log it should of been fixed in november (November 6th
to be exact):

Although again, I haven't tested it so take what I say with a grain of salt.

Jeff Wereszczynski
Assistant Professor of Physics
Illinois Institute of Technology

On Fri, Apr 11, 2014 at 11:39 AM, Francesco Pietra <> wrote:

> Hi Jeff:
> accelMD on GPUs was not advertised, as far as I know. If it was activated
> in the nightly builds of either 2.9 or 2.10 would be great. We are loosing
> a lot of time by using CPUs only. Hope developers would like to confirm. I
> asked some days ago about a rough date for namd being able to compute
> energies on GPUs, having no answer.
> cheers
> francesco pietra
> On Fri, Apr 11, 2014 at 2:19 PM, Jeff Wereszczynski <>wrote:
>> 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.
>> Cheers,
>> Jeff
>> 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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