From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Wed Sep 10 2014 - 02:13:00 CDT
Hi Tristan,
It is likely that NAMD was just about scaled out in your previous setup,
and the extra communication necessary to gather the coordinates of 1500
atoms is killing that scaling. Effectively, you are introducing long-range
interactions involving a large number of atoms. The only way out of this is
to reduce the number of atoms involved.
Best,
Jerome
On 10 September 2014 03:31, Tristan Croll <tristan.croll_at_qut.edu.au> wrote:
> Hi all,
>
>
>
> I’m currently running what’s effectively a TMD simulation based on the
> colvars file pasted in below. Briefly, I have two domains which were
> previously steered to within ~30 angstroms between their centres of mass,
> and are now allowed to rattle around within a wall at 31 angstroms. That
> initial steering simulation ran well (and fast) even with the inclusion of
> four individual RMSD colvars with harmonic restraints maintaining the
> internal fold of individual domains.
>
>
>
> In the current phase, I’m steering two other groups of atoms – one of
> which I’m maintaining to the geometry it “found” during the previous phase
> of the simulation, while the other is steered to a matching configuration
> over 20ns. There’s nothing fundamentally different about this simulation
> from what I’ve done to date, yet it’s consistently running ~8-fold slower.
> Just wondering what might be causing this? The only real differences I see
> are the number of atoms in each colvar (~1500 in this case vs ~50
> previously – I’m steering all heavy atoms this time around, rather than
> just restraining CAs), and the fact that while the individual atoms in each
> of the current colvars I’m steering are fairly close in 3D space, they’re
> up to a few thousand residues apart in the sequence.
>
>
>
> Is this slowdown likely to be a consequence of my setup, or should I look
> more closely at the cluster? The managers of it assure me there’s nothing
> currently going wrong there...
>
>
>
> Thanks,
>
>
>
> Tristan
>
>
>
>
>
> colvarsTrajFrequency 1000
>
> colvarsRestartFrequency 1000
>
>
>
> colvar {
>
> name Fn_distance
>
>
>
> outputAppliedForce on
>
> upperWall 31.0
>
> upperWallConstant 10
>
>
>
> distance {
>
> group1 {
>
> atomsfile colvars.pdb
>
> atomsCol O
>
> atomsColValue 1.0
>
> }
>
>
>
> group2 {
>
> atomsfile colvars.pdb
>
> atomsCol O
>
> atomsColValue 2.0
>
> }
>
>
>
> forceNoPBC yes
>
> }
>
> }
>
>
>
>
>
>
>
>
>
> colvar {
>
> name RMSD_ID_E
>
>
>
> rmsd {
>
> atoms {
>
> atomsfile target_ID_sym.pdb # Select biased atoms from this file
>
> atomsCol B # based on beta
>
> atomsColValue 1.0
>
> }
>
> refPositionsFile target_ID_sym.pdb # ref. positions are selected based
> on atom number
>
> }
>
> }
>
>
>
> harmonic {
>
> name ID_E_restrain
>
> colvars RMSD_ID_E
>
> centers 0
>
> targetCenters 0
>
> targetNumSteps 25000000
>
> forceConstant 10
>
>
>
> }
>
>
>
> colvar {
>
> name RMSD_ID_F
>
>
>
> rmsd {
>
> atoms {
>
> atomsfile target_ID_sym.pdb # Select biased atoms from this file
>
> atomsCol B # based on beta
>
> atomsColValue 2.0
>
> }
>
> refPositionsFile target_ID_sym.pdb # ref. positions are selected based
> on atom number
>
> }
>
> }
>
>
>
> harmonic {
>
> name ID_F_steer
>
> colvars RMSD_ID_F
>
> centers 4.8
>
> targetCenters 0
>
> targetNumSteps 10000000
>
> forceConstant 10
>
>
>
> }
>
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