Yes - pmemd would have the exact same problem. The step integration
algorithms are pretty much the same as sander, and I have not made any
attempts to allow for a changing stepsize.
Regards - Bob Duke
----- Original Message -----
From: "David A. Case" <case.biomaps.rutgers.edu>
To: <amber.scripps.edu>
Sent: Tuesday, November 18, 2008 7:13 AM
Subject: Re: AMBER: SPCFW temperature oscillations
> On Mon, Nov 17, 2008, Naser Alijabbari wrote:
>
>> Using SPCFW, I have only been able to run a 'production run' with an
>> integration time step of 2fs. Lower times (1fs or .25fs) result in wild
>> fluctuations of temperature and energy. Here is what I have tried:
>>
>> After 100ps of adjusting my density using this input file:
>>
>> &cntrl
>> ntt = 3, gamma_ln = 1.0,
>> nstlim = 50000, dt = 0.002,
>> &end
>>
>>
>> Then I tried running a 10ps test production run using Berendsen algorithm
>> and 1fs integration time but my energy and temperature fluctuated from
>> 300K
>> to ~330K. I thought my time step was too large so I tried .25fs
>> integration
>> time:
>>
>> &cntrl
>> imin = 0, irest = 1, ntx = 5,
>> ntb = 2, pres0=1.0, ntp=1,
>> ntt = 1, nscm=0,
>> nstlim = 40000, dt = 0.00025,
>> ntpr = 1, ntwx = 6, ntwr = 1000,
>> &end
>>
>> &ewald
>> ew_type=0, dsum_tol=0.000001
>> &end
>>
>
> Sander (and also pmemd, I think) does weird things when you "restart" a
> simulation with a different time step -- basically, it does not know that
> the
> input velocities were created with a different time step, so you usually
> have
> to re-equilibrate at the new time step, at least for a short while.
>
> My guess is that the 2fs time step with SPCFW was actually unstable, but
> that
> the Langevin thermostat was hiding that fact. When you then switched to a
> very weak coupling thermostat and changed the time step, the instability
> surfaced.
>
> I've never used SPCFW myself, but my guess is that something like a 0.5fs
> time
> step is required. Try equilibrating (say with ntt=3) using that time
> step,
> then changing to NVE or ntt=1.
>
> [If you have a solute, like a peptide or protein, you should also be aware
> that protein-water interactions using SPCFW have not been tested nearly as
> much as for rigid water models. So, be sure to proceed with caution.]
>
> ...dac
>
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Received on Fri Dec 05 2008 - 15:52:25 PST
