AMBER Archive (2006)

Subject: Re: AMBER: QM/MD energy conservation

From: Gustavo Seabra (gustavo.seabra_at_gmail.com)
Date: Tue Dec 12 2006 - 08:02:39 CST

Hi Evan,

Did you equilibrate you system using QM or MM?

Also, you may have to tighten the scf convergence criterion (see
scfconv and tight_p_conv in Amber manual) to achieve better energy
conservation.

Gustavo.

On 12/11/06, Evan Kelly <ebkelly_at_ualberta.ca> wrote:
> Hi Everyone,
>
> I am hoping to use Amber9 to perform some QM/MD simulations of a molecule
> (treated quantum mechanically) in a box of classical (TIP3P) water
> molecules. After warming and equilibrating my system, I decided to test my
> timestep by running the system under NVE conditions (ie. ntb=1, ntt=0,
> ntp=0). I am surprised by the results: during a 20ps run, the total energy
> steadily rises by about 120kcal/mol (this is about 100 from the potential
> energy and about 20 from the kinetic energy). My guess is that this
> indicates a problem somewhere. The problem appears to be with the QM
> portion of the simulation, as the identical run with ifqnt=0 conserves
> energy almost perfectly. The QM energy does seem to be more or less
> conserved, though. The same problem exists for dt = 1, 1.5, and 2, as well
> as for both the AM1 and PM3 QM flavors. Nothing unusual is visible upon
> viewing the trajectory of the simulation. I have included my input file
> below.
>
> I'd appreciate any suggestions or comments anyone can make about this
> potential problem. Thanks!
>
>
>
> -----input file-------
>
> Minimization of water molecules of VLB (1Z2B structure) in TIP3P box
> &cntrl
> imin = 0,
> irest = 1,
> ntx = 7,
> ntb = 1, !Constant volume simulation while testing E conservation
> pres0 = 1.0,
> ntp = 0, !no barostat while testing E conservation
> taup = 2.0,
> ntc = 2, !says to SHAKE H-X bond lengths, needed for TIP3P water
> ntf = 2, !says to skip H-X bond calculations, again needed for TIP3P
> water
> cut = 10,
> dielc = 1,
> tempi = 300.0,
> temp0 = 300.0,
> ntt = 0, !constant energy simulation to test conservation w/ dt
> nstlim = 10000, dt = 0.002,
> ifqnt = 1, !TURN ON QM/MM
> ntpr = 50, ntwx = 100, ntwr = 500, ntwe = 50,
> /
> &qmmm
> qmmask = ':VLB', !which atoms are treated with QM
> qmcharge = 0,
> qmtheory = 1, !use the PM3 hamiltonian
> qmshake = 1, !use shake on the QM atoms
> qm_ewald = 1,
> qm_pme = 1,
> spin = 1,
> printcharges = 1,
> writepdb = 1,
> /
>
>
>
>
>
> ----------------------------------
> Evan Kelly
> ebkelly_at_ualberta.ca
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu