[gmx-developers] constraining velocities

[Erik Lindahl]

Hi Berk,

Very nice. This might actually help explain the strange energy  
conservation patterns with mixed single/double precision constraints  
too, where we had to do both integration and constraints in double to  
get good conservation.

If you send me the tetrapeptide I can try to rerun it when we do only  
constraints + velocity correction in double (unless you feel like  
doing it yourself :-)

Cheers,

Erik



On Oct 16, 2006, at 3:11 PM, Berk Hess wrote:

> Hi,
>
> After speaking with several people at the computational chemistry  
> Gordon conference
> 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  
> velocities
> 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
>
> settle
> 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.
>
> Berk.
>
> _______________________________________________
> gmx-developers mailing list
> gmx-developers at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-developers
> Please don't post (un)subscribe requests to the list. Use the www  
> interface or send it to gmx-developers-request at gromacs.org.