Thank you everyone.
*******************************
Mohd Farid Ismail
Graduate Student
Dept. of Chemistry/Biochemistry
University of Oklahoma
Norman 73019
________________________________________
From: Jason Swails [jason.swails.gmail.com]
Sent: Sunday, December 30, 2012 10:34 AM
To: AMBER Mailing List
Subject: Re: [AMBER] NPT and NVE Energy
Since the issue of energy conservation has already been well addressed,
I'll make a quick comment about using SHAKE. If you are using a rigid
water molecule (e.g., TIP3P, TIP4P, TIP4Pew, SPCE, etc.), you should
constrain at least the hydrogen-containing bonds in the water molecules or
be prepared to defend your choice not to if you publish.
You can use the "noshakemask" variable to remove SHAKE from your solute if
you want.
HTH,
Jason
On Sun, Dec 30, 2012 at 9:19 AM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Sun, Dec 30, 2012, Ismail, Mohd F. wrote:
> > This is my input file. Can you comment if there is any bad parameter?
> >
> > production run
> > &cntrl
> > imin=0, irest=1, ntx=5,
> > nstlim=40000000, dt=0.0005, ntc=1,
> > ntpr=2000, ntwx=2000, ntwr=-1000000,
> > ntwv=2000, ntwe=2000,
> > ntt=0, tempi=300.0, temp0=300.0, ntp=0, ntb=1,
> > cut=10, iwrap=1,
> > &end
>
> Looks OK to me; you might experiment to see what turning on SHAKE does
> (set tol=0.000001 or so). Also, set dsum_tol to 10**-6 (in the &ewald
> namelist); regardless of shake, that should help with energy
> conservation.
>
> >
> > The system contains 32500 atoms.
> > > The energy drift is linear, which makes me wonder why. If the system
> is
> > > not fully equilibrated, I expect it to be random. The change in
> energy is
> > > like 20kcal/mol for 20ns. Is this bad?
>
> I don't think this is bad. Note that 20 kcal/mol is a tiny fraction of a
> degree for a system with 32500 * 3 degrees of freedom. So your drift
> seems within the range of what people usually live with. To put it in
> terms Andreas used (see snippet below) you are seeing 1.5 x 10**-9
> kT/ns/dof, which is smaller than that often seen, maybe because your
> cutoff is 10 Ang rather than 8 (the default).
>
> ....dac
>
> >From Andreas Goetz:
>
> The energy drift will depend on details of the simulation (energy
> conservation is actually not a trivial topic). Using AMBER, for explicit
> solvent calculations using PME, I have typically seen fairly linear
> energy drifts +between 1.E-07 (0.5fs time step, no SHAKE) and 1.E-05
> (2.0fs time step, with SHAKE) in units of kT/ns/dof at 300K (dof = degree
> of freedom). This translates to something between 0.5 kcal/mol and 25
> kcal/mol for 20ns for a system with +100k atoms.
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Jan 01 2013 - 21:30:03 PST
