Dear Ananda
You can find several answers to your question by going to the amber mailing
list archive:
http://amber.ch.ic.ac.uk/archive/
And entering "Increase lastrst in the &cntrl namelist" into the search box
there. You could also just try following what the instructions say and
putting lastrst=xxx in the &cntrl namelist and then simply keep increasing
this value until the error stops.
However, you have other problems with your simulation that I would address
first:
> dielc = 1.00000, cut = 5.00000, intdiel = 1.00000
This is an unrealistically small cutoff for a simulation. For periodic
boundary PME simulations (ntb=1) the minimum should be 8.0. You should NEVER
go lower than this under any circumstances. Even if your system is huge and
you can't afford the computer time. You results will be largely meaningless
if the cutoff is smaller than 8.0 angstroms here. When you set cut=8.0 you
may find that the lastrst error goes away.
For non-periodic simulations ideally you should use no cut off at all (I.e.
set cut=999.0, or simply much larger than the extent of your system).
However, this can be very expensive. For gas phase calculations you should
probably never use a cut off. For Implicit solvent simulations however you
can usually get satisfactory results with a cutoff of 16 angstroms or
larger. Although typically you would want a minimum of 18 angstroms or so.
> ntf = 1, ntb = 1, igb = 0,
> t = 0.00000, dt = 0.00100, vlimit = 20.00000
Is there a reason you are not using shake (ntc=1, ntf=1)? Most of the rigid
water models will give incorrect results if shake is not used. Also 1fs is
really the upper limit for the time step when shake is not in use. 0.5 fs
would be safer. Alternatively you should probably consider setting shake on
(ntc=2, ntf=2) and setting dt to between 1.5 and 2.0fs.
> Berendsen (weak-coupling) temperature regulation:
> temp0 = 300.00000, tempi = 300.00000, tautp = 1.00000
The Berendsen thermostat is no longer recommended. If you are using amber 8
or amber 9 you would be better using langevin dynamics (ntt=3) for your
heating and equilibration phase and then no thermostat at all (ntt=0) for
the production phase. See page 95 of the Amber 9 manual for more info.
(
http://amber.scripps.edu/doc9/index.html)
All the best
Ross
/\
\/
|\oss Walker
| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk | PGP Key available on request |
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Received on Wed Apr 19 2006 - 06:07:06 PDT
