Re: ABF/colvar error in NAMD2.9

From: Harish Vashisth (harish.vashisth_at_gmail.com)
Date: Tue Jul 22 2014 - 14:39:15 CDT

Thanks everyone for suggestions. We will try those things.

On Tue, Jul 22, 2014 at 2:32 PM, Niklaus Johner <niki.johner_at_gmail.com>
wrote:

> To increase sampling of dihedrals you could also try accelerated MD.
> Another option available in the plumed plugin (http://www.plumed-code.org/)
> could be to use the AlphaRMSD and BetaRMSD collective variables which would
> basically bias the percentage of the peptide in the alpha and beta
> conformation.
>
> Except if you are doing implicit solvent simulations, I would avoid
> temperature replica exchange. It's a waste of resources.
>
> Best,
>
> N.
>
> On Jul 22, 2014, at 8:08 PM, Aron Broom wrote:
>
> 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
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> 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
>
>
> Dr Niklaus Johner
> Weill Cornell Medical College
> Harel Weinstein Lab
> Department of Physiology and Biophysics
> 1300 York Avenue, Room D-501
> New York, NY 10065
>
>
>
>

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