Hi,
I took Dr. Case's recommendation and run a 10 step simulation. The test case did not pass, it was running and I tried to tail -f the .out file, but nothing showed up. The simulation ran for the entire weekend and there's no output file so I stopped it.
What do you think the problem is?
With regards,
Yang
> From: carlos.simmerling.gmail.com
> Date: Mon, 29 Mar 2010 15:58:40 -0400
> Subject: Re: [AMBER] simulation under pressure
> To: amber.ambermd.org
>
> have the test cases passed? is the job still getting CPU time? do you get
> any output at all?
>
> On Mon, Mar 29, 2010 at 3:53 PM, Yang Li <chlorin316.hotmail.com> wrote:
>
> >
> > Hi, Dr. Case,
> >
> > Thank you for you recommendations. I checked and my prmtop was
> > periodic and solvated. I tried to run a 10 step simulation, here is my
> > input file.
> >
> > DNA 12-ATmer simulation under 100atm
> > &cntrl
> > imin = 0, irest = 1,
> > igb = 0, ntx = 5,
> > ntt = 3, gamma_ln = 1.0,
> > tempi = 300.0, temp0 = 300.0
> > ntp = 1, taup = 2.0, pres0 = 100,
> > ntb = 2, ntc = 2, ntf =2,
> > nstlim = 10, dt = 0.01
> > ntwx = 1, ntpr =1
> > cut = 12.0
> > /
> >
> >
> > However, the simulation has run for the entire weekend again and did
> > not finish on the 3G processor.
> >
> > Please let me know what I can do.
> >
> >
> > With regards,
> >
> > Yang
> > _________________________________________________________________
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Received on Mon Mar 29 2010 - 19:00:03 PDT
