From: Kevin Kastner (kkastner_at_nd.edu)
Date: Fri Apr 11 2014 - 13:06:28 CDT
I am using NAMD version 2.8 with CUDA. So I guess that version of aMD is
not working properly with GPUs, huh? Ok, I will need to try it on the CPUs
and see if that works. Thanks all!
Also, Felipe: I will take a look at that paper and see about the parameters
that they use and compare them to mine. Thank you!
On Fri, Apr 11, 2014 at 1:16 PM, Francesco Pietra <
francesco.pietra_at_accademialucchese.it> wrote:
> Thanks. I'll try as soon as running accelMD will end, comparing with
> results from cpus alone, if it works.
>
>
> On Fri, Apr 11, 2014 at 6:50 PM, Jeff Wereszczynski <jwereszc_at_iit.edu>wrote:
>
>> According to the CVS log it should of been fixed in november (November
>> 6th to be exact):
>>
>> http://www.ks.uiuc.edu/Research/namd/cvs2html/chronological.html
>>
>> 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
>> http://www.iit.edu/~jwereszc
>>
>>
>> On Fri, Apr 11, 2014 at 11:39 AM, Francesco Pietra <
>> francesco.pietra_at_accademialucchese.it> 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 <jwereszc_at_iit.edu>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
>>>> http://www.iit.edu/~jwereszc
>>>>
>>>>
>>>> On Fri, Apr 11, 2014 at 3:27 AM, Felipe Merino <
>>>> felipe.merino_at_mpi-muenster.mpg.de> 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
>>>>>
>>>>>
>>>>>
>>>>
>>>
>>
>
-- - 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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