On Thu, Nov 29, 2012 at 8:44 AM, Fabian Glaser <fglaser.technion.ac.il>wrote:
> Works!!
>
> I am running production dynamics as in the tutorials (first time), so
> allow me to ask you if this settings are good for a medium size protein
> (130 aa) with 6000 waters. For 30 ns ....
>
> production dynamics
> &cntrl
> imin=0, irest=1, ntx=5,
> nstlim=15000000, dt=0.002,
> ntc=2, ntf=2,
> cut=10.0, ntb=2, ntp=1, taup=2.0,
> ntpr=1000, ntwx=1000, ntwr=50000,
> ntt=3, gamma_ln=2.0,
> temp0=300.0,
> /
>
A few comments here:
1) Constant pressure MD is noticeably slower than constant volume MD (since
NPT requires calculating the virial). While you should always use NPT at
some point in your simulation, I typically restrict this to my
equilibration stage and wait until the density (or box size) stabilizes.
Once this occurs, NPT and NVT are more or less indistinguishable in
aqueous solvent (since water is approximately incompressible).
2) I discourage you from trying to run something like 30 ns of simulation
at once (unless you're simulating <100 atoms or something). I typically
run simulations in chunks of 1 or 2 ns. The benefit of this approach is
that you can submit shorter jobs which are more likely to start in most
clusters. You can also submit the jobs in such a way that you submit 30
1-ns jobs at once, and each one is held from running until the job in front
of it finishes. This kind of approach is far less susceptible to being
killed by a node failure and will likely finish much faster.
For an introduction on using PBS effectively, see
http://jswails.wikidot.com/using-pbs
Good luck,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Nov 29 2012 - 07:30:02 PST
