From: Niklaus Johner (niki.johner_at_gmail.com)
Date: Tue Jul 22 2014 - 13:32:12 CDT
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).
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> 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.
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> 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:
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> abf {
> colvars phi1 psi1 phi2 psi2 phi3 psi3 phi4 psi4
> fullSamples 100
> }
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> We have also tried using "metadynamics" as a bias in NAMD with similar memory error message with large number of CVs.
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> -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.
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> 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.
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> On Tue, Jul 22, 2014 at 12:56 PM, Jrme Hnin <jerome.henin_at_ibpc.fr> wrote:
> Aron, when you ahd 9 colvars, maybe they were not assigned a single ABF bias?
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> 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.
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> 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:
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> FATAL ERROR: Memory allocation failed on processor 0.
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> 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?
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> 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?
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> Any suggestions would be helpful. Thanks.
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> -Harish
> --------------
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> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
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> --
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
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> --
> 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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