Re: Accelerated MD with transmembrane protein

From: Francesco Pietra (
Date: Sat Apr 12 2014 - 08:24:00 CDT

accelMD with 64bit multicore cuda 2014-04-12 works well, very fast, on
GNU-Linux Debian amd64, multiple GTX680. To check whether it will agree
with accelMD on CPUs alone will take time.

It was not a matter of "a grain of salt". Either it worked or not.

Thanks again for having informed about that fix

On Fri, Apr 11, 2014 at 6:50 PM, Jeff Wereszczynski <>wrote:

> 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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