From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Fri Feb 21 2014 - 01:34:55 CST
This is interesting. I've never observed such a runaway behavior while using
Amber, maybe this is a hint. Additionally, are you guys, having this
problem, using ECC enabled machines and GPUs.
Norman Geist.
> -----Ursprüngliche Nachricht-----
> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> Auftrag von Tristan Croll
> Gesendet: Freitag, 21. Februar 2014 00:52
> An: namd-l_at_ks.uiuc.edu
> Betreff: namd-l: RE: Runaway positive feedback when minimizing large
> systems (was: strange glitches when performing energy minimization in
> MDFF simulations)
>
> Minor error correction: sentence below should read "... had undergone
> extensive *equilibration*..."
>
> -----Original Message-----
> From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On
> Behalf Of Tristan Croll
> Sent: Thursday, 20 February 2014 9:54 AM
> To: Bennion, Brian; Norman Geist; namd-l_at_ks.uiuc.edu
> Subject: namd-l: RE: Runaway positive feedback when minimizing large
> systems (was: strange glitches when performing energy minimization in
> MDFF simulations)
>
> Hi all,
>
> Just wondering if anyone's had a chance to look at this?
>
> My own observations from watching a few different-sized simulations
> minimize in IMD Connect after doing various perturbations to different
> residues:
>
> - For some reason that's not entirely clear (perhaps floating-point
> errors as the total system energy gets very large?), minimization in
> general gets more "jumpy" (i.e. atoms move further with each
> minimization step) as the system size increases;
>
> - In some (fairly rare) cases, this leads to a temporary runaway in the
> algorithm as a small initial deviation is magnified into a very large
> local disturbance, which can lead to cis/trans or chirality flips
> before settling;
>
> - The "runaway" effect seems to only occur in a few different
> situations - so far I've only been able to replicate it reliably in
> solvent-exposed asparagine residues (by changing the length of the
> side-chain C=O bond) and in histidines (by moving the side-chain
> nitrogens slightly closer together). Similar scale changes in other
> residues still lead to transient deviations larger than what one would
> expect to see in a smaller-scale simulation, but these are usually
> brought under control quite quickly (I've by no means done an
> exhaustive check of different residues, though). In both the asparagine
> and histidine cases, I've seen such runaways arise in re-minimization
> of structures that had undergone extensive minimization, indicating
> that structural deviations within (but at the outskirts of) normal
> ranges can trigger the problem.
>
> - I've replicated the same behaviour in NAMD versions 2.8 and 2.9, on a
> cluster (ibverbs) build and on my local workstation, in both CUDA and
> non-CUDA builds, and in both CHARMM 27 and 36 forcefields.
>
> - Perhaps most strangely, I had more trouble replicating the runaway
> behaviour in the STMV benchmark than in the ATPase benchmark.
>
> Anyway, a fairly straightforward workaround for anyone who's worried is
> to always do a few thousand steps of backbone-restrained minimization
> first, even if you're just re-minimizing a previously equilibrated
> system.
>
> Cheers,
>
> Tristan
>
> -----Original Message-----
> From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On
> Behalf Of Tristan Croll
> Sent: Thursday, 13 February 2014 9:51 AM
> To: Bennion, Brian; Norman Geist; namd-l_at_ks.uiuc.edu
> Subject: namd-l: RE: Runaway positive feedback when minimizing large
> systems (was: strange glitches when performing energy minimization in
> MDFF simulations)
>
> Hi Brian,
>
> I'll go one better. At the link below I've put together a
> demonstration simulation. It's based on the ATPase benchmark, and the
> only thing I've done is moved the OD1 atom on ASN33 of segname PSLN by
> roughly 0.2A.
>
> - Untar into a directory of your choice
> - load f1wations_xplor.psf / f1wations-pme-nve-
> 200ps_PSLN_33_OD1_moved.pdb in VMD
> - visualise "segname PSLN and resid 33" and "same residue as within 10
> of (segname PSLN and resid 33)" in your choice of representation, and
> center your view on the former
> - run namd using the config file f1atpase.namd
> - In VMD, go to Extensions/Simulation/IMD Connect
> - enter "localhost" in the Hostname box and 2030 in the Port box
> - after allowing some time for the simulation to set itself up, click
> Connect
> - enjoy (?) the show.
>
>
>
> Cheers,
>
> Tristan
>
> https://www.dropbox.com/s/zqa9qwy60v2bd4x/f1atpase_min_glitch.tar.gz
>
>
>
> -----Original Message-----
> From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On
> Behalf Of Bennion, Brian
> Sent: Thursday, 13 February 2014 2:57 AM
> To: namd-l_at_ks.uiuc.edu
> Subject: namd-l: RE: Runaway positive feedback when minimizing large
> systems (was: strange glitches when performing energy minimization in
> MDFF simulations)
>
> Hello Tristan,
>
> In one of you posts you showed a histidine oscillating. can this be
> replicated with any histidine in your autoimd tests?
>
> Does the asp need to be in the center of the box to be show the
> behaviour?
> Would you mind posting your autoimd config files and I will have a go
> at it
>
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