From: Marcos Sotomayor (sotomayo_at_ks.uiuc.edu)
Date: Thu Mar 08 2007 - 07:17:57 CST
Hi Anna,
The lack of energy conservation in your simulations likely arises from the
use of a multiple-time stepping algorithm (your electrostatic
interactions are being computed every 4 femtoseconds). Change your
fullElectFrequency to 1 (keeping the 2fs timestep) and you should see an
improvement in your energy conservation. The resonance causing
this problem (and the use of Langevin dynamics to avoid it in some cases)
is well documented in papers of Bob Skeel.
Regards,
Marcos
On Tue, 6 Mar 2007, ahenneck_at_ix.urz.uni-heidelberg.de wrote:
> Dear NAMD users
>
> I observe a total energy increase of about 70kcal/ns in my NVE dynamics
> simulations (TOTAL, TOTAL2 and TOTAL3 are increasing, potential and kinetic
> energy are stable).
> This does not occur with a timestep of 1 fs, however since I fix all bonds to
> hydrogen atoms, a 2fs timestep should work as well.
>
> If anybody has run stable NVE simulations using the CHARMM22 force field, I'd
> be happy to get the simulation parameters optimized to this force field or a
> suggestion on how to better conserve the total energy.
>
> Cheers
> Anna
>
> My setup:
> - short (11 residue) aspartic-acid-rich peptide in explicit water (periodic
> boundary conditions)
> - The system was heated slowly. Equilibration was done in three steps,
> gradually releasing constraints from the peptide and using velocity rescaling
> every 500 timesteps
>
> #############################################################
> ## SIMULATION PARAMETERS ##
> #############################################################
>
> # Input
> paraTypeCharmm on
> parameters /home/par_all22_prot.inp
> # temperature 300
>
> # Force-Field Parameters
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 10.
> switching on
> switchdist 9.
> pairlistdist 11.5
>
>
> # Integrator Parameters
> timestep 2.0
> rigidBonds all
> nonbondedFreq 1
> fullElectFrequency 2
> stepspercycle 10
>
>
> # Constant Temperature Control
> langevin off
> #langevinDamping 1
> #langevinTemp 300
> #langevinHydrogen off
>
>
> # Periodic Boundary Conditions
> cellBasisVector1 70. 0. 0.
> cellBasisVector2 0. 70. 0.
> cellBasisVector3 0. 0 70.
> cellOrigin 0. 0. 0.
>
> # Image center all molecules
> wrapAll on
> wrapNearest on
>
> # PME (for full-system periodic electrostatics)
> PME yes
> PMEGridSizeX 61
> PMEGridSizeY 61
> PMEGridSizeZ 61
> # Order default 4 (cubic):
> PMEInterpOrder 6
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