On Sat, Feb 25, 2012, amir abbasi wrote:
>
> When I'm running a simulation in explicit water,I have face an unusual thing.
> My system sticking in a step of simulation and not going forward.
> what is cause this problem?
> My Input File:
> initial relaxation of 5nt ribozyme
> &cntrl
> imin = 0,irest =1, ntx = 7,
> tempi = 300.0, temp0 = 300.0,
> ntp = 1,
> ntt = 3, gamma_ln =1,
> ntb = 2,
> ntc = 2, ntf = 2,
> nstlim = 10000000,dt = 0.002,
> ntpr = 100, ntwx = 100, ntwr = 1000,
> cut = 12
> /
There is nothing obviously wrong with the above input, although using a cutoff
of 12 is unusally large (and expensive), probably for no gain in accuracy.
You don't say when it "sticks", or what partial output you received. I'd
suggest reducing nstlim by 5 orders of magnitude, setting ntpr=1, and trying
again. If that works, you can slowly increase the number of steps and try to
debug.
[I'm really guessing here, since you gave so little information! You have
irest=1, so I'm assuming that you have some previous runs that worked, and
that the system has been equilibrated, otherwise it would not make much sense
to request a 20 ns run. Asking for 10 million steps is something that only
makes sense when you are pretty sure that everything is fine with your system,
which is not the case here.]
....dac
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Received on Sat Feb 25 2012 - 07:00:02 PST
