AMBER Archive (2009)
Subject: Re: [AMBER] problem with the results in the .out file!
From: Gustavo Seabra (gustavo.seabra_at_gmail.com)
Date: Tue Mar 31 2009 - 08:01:41 CDT
On Tue, Mar 31, 2009 at 1:30 AM, Aravind S
> Dear Users,
> I am facing another problem with my simulation.
> I was trying to simulate 227d.pdb with the following parameters:
> there are no constraints involved.
> I ran the 50 ps simulation with a 10fs time step,
Is that really correct? Thats way above the maximum recommended time
step. If you are using shake, the recommended maximum for the rime
step is 2 fs.
> temp remaining constant at 300K.
> By default my ntx=7 and irest=1.
By default, ntx=1, irest=0.
> My .rst file used was the result got through my previous simulation.
> My problem is that the .rst file isnt being generated ,
> only the .mdcrd and the .out files got generated and the .mdcrd files
> had nothing written on it.
That's not surprising, assuming you really used a 10fs timestep. The
simulation probably never reached the point of writing the restart
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