From: Aron Broom (broomsday_at_gmail.com)
Date: Tue Jul 22 2014 - 13:08:48 CDT
I'm not sure of the titles, but there are some other works on small
peptides, where they use a smaller collection of CVs to try and get at the
same information one might have through the full dihedral biasing. For
instance, I think they would use backbone RMSD, radiusOfGyration, and one
other CV to try and get a general descriptor of the structural
configuration, without needing to explicitly handle all the dihedrals.
Just a thought (you could even break the peptide up into a few RMSD
colvars).
On Tue, Jul 22, 2014 at 2:00 PM, Harish Vashisth <harish.vashisth_at_gmail.com>
wrote:
> Hi Jerome, Aron:
> Thanks for your suggestions. I did a quick test. Previously, we were
> using the width parameter of 5 for sampling between 0 and 180 of each
> dihedral angle CV. I experimented with increasing this to 10 and 20, which
> allows usage of more (read 8) CVs (Not that it is scientifically meaningful
> or will give useful information). So as Jerome suggests memory issue is
> sensitive to binwidth which is coupled with large number of CVs as each CV
> is to be sampled.
>
> Aron: i double checked that our definitions of CVs are correctly written;
> I think the error was not due to wrong syntax. Also, i appreciate the issue
> with sampling many CVs, but thought something on the order of 20 may be
> possible with abf. We were experimenting with running abf calculation using
> backbone dihedrals of a 12-15 residue peptide. we were also using a single
> ABF bias on all CVs in this test case like below:
>
> abf {
> colvars phi1 psi1 phi2 psi2 phi3 psi3 phi4 psi4
> fullSamples 100
> }
>
>
> We have also tried using "metadynamics" as a bias in NAMD with similar
> memory error message with large number of CVs.
>
> -Harish
>
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> On Tue, Jul 22, 2014 at 1:32 PM, Aron Broom <broomsday_at_gmail.com> wrote:
>
>> Jerome: You are certainly correct, I hadn't thought is was a single
>> massively-dimensional bias. The memory thing makes much more sense now, as
>> per your equation.
>>
>> Harish: Memory issues aside then, I don't think you would ever be able to
>> reach equilibrium with such a massive coordinate space to bias across. If
>> you look at Jerome's equation it not only relates to memory usage, but is
>> also proportional to how many timesteps you would need to sample
>> everything. The unfortunate truth is that given current technology, brute
>> forcing a problem like this (trying to explore over all the conformations)
>> just isn't possible. You need to do something that is less explicit in
>> it's biasing, like replica exchange or some other form of accelerated
>> sampling that doesn't require the full exploration of the coordinate space.
>>
>>
>>
>>
>> On Tue, Jul 22, 2014 at 12:56 PM, Jérôme Hénin <jerome.henin_at_ibpc.fr>
>> wrote:
>>
>>> Aron, when you ahd 9 colvars, maybe they were not assigned a single ABF
>>> bias?
>>>
>>>
>>> On 22 July 2014 18:30, Aron Broom <broomsday_at_gmail.com> wrote:
>>>
>>>> I've used an upwards of 9 colvars at once with no issue, and with a
>>>> larger system size than that. Can you post the *.in file or whatever file
>>>> contains all your colvars definitions? I would suspect something add with
>>>> your colvars. One thing to test might be, when you are at the largest size
>>>> that has worked (I guess 4 colvars?) try just duplicating all those colvar
>>>> blocks and see if it runs. Maybe something is wrong with the 5th colvar
>>>> definition you are entering.
>>>>
>>>>
>>>> On Tue, Jul 22, 2014 at 12:23 PM, Harish Vashisth <
>>>> harish.vashisth_at_gmail.com> wrote:
>>>>
>>>>> Dear All:
>>>>> We have been trying to make use of many CVs (> 20) using abf/colvar
>>>>> options in NAMD2.9. These are all backbone dihedral CVs defined
>>>>> individually in multiple blocks of phi/psi, etc. We are able to run ABF
>>>>> jobs fine up to 5 CVs, but including a sixth one or more does not work. The
>>>>> error reported in the log file right after initialization of colvars module
>>>>> is:
>>>>>
>>>>> FATAL ERROR: Memory allocation failed on processor 0.
>>>>>
>>>>> Looking through previous posts, someone seemed to suggest that it is
>>>>> likely occurring due to large system size as NAMD keeps a copy of the
>>>>> system on processor 0?
>>>>>
>>>>> In our case, the solvated system size is ~40,000 atoms. The error
>>>>> occurs using NAMD2.9 on local workstation, our local CRAYXE6m-200 as well
>>>>> as on Stampede (XSEDE resource.) Is there an upper limit on how many CVs
>>>>> colvar module can handle?
>>>>>
>>>>> Any suggestions would be helpful. Thanks.
>>>>>
>>>>> -Harish
>>>>> --------------
>>>>>
>>>>>
>>>>
>>>>
>>>> --
>>>> Aron Broom M.Sc
>>>> PhD Student
>>>> Department of Chemistry
>>>> University of Waterloo
>>>>
>>>
>>>
>>
>>
>> --
>> Aron Broom M.Sc
>> PhD Student
>> Department of Chemistry
>> University of Waterloo
>>
>
>
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
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