[gmx-developers] constraining velocities
dmobley at gmail.com
Mon Oct 16 16:10:21 CEST 2006
Thanks for taking a look at this! It looks like you're making headway.
This is good news.
On 10/16/06, Berk Hess <hessb at mpip-mainz.mpg.de> wrote:
> After speaking with several people at the computational chemistry Gordon
> I realized that Gromacs loses a lot of accuracy when using constraints
> by doing:
> v_(n+1/2) = (x_(n+1) - x_(n))/dt
> I have now fixed this (in the development branch) by correcting the
> using the Lagrange multipliers of the constraints.
> The error still increases with decreasing timestep, but it has decreased
> a lot.
> I have done some NVE tests with
> single precision v_(n+1/2) = (x_(n+1) - x_(n))/dt (first column)
> single precision with the new velocity correction (second column)
> double precision (last column)
> The results are the drift in the total energy in kJ/mol /ns /dof
> tetrapeptide in vacuum, flexible, nrdf: 123
> dt=0.001 0.04 <0.01 <0.01
> tetrapeptide in vacuum, bond-constraints, nrdf: 82
> shake tol=1e-5
> dt=0.002 4.64 -0.18 -0.29
> lincs iter=2, order=8
> dt=0.001 2.73 0.27 <0.01
> dt=0.002 0.47 0.13 <0.01
> 216 SPC, nrdf: 1293
> dt=0.001 -0.14 -0.04
> dt=0.002 -0.06 -0.02
> dt=0.004 0.01 0.01
> Especially shake seems to profit from this change.
> Velocity verlet seems to be more accurate than the old Gromacs code,
> but less accurate than my new code.
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