AMBER Archive (2009)

Subject: Re: [AMBER] problem with the results in the .out file!

From: Aravind S (
Date: Thu Apr 02 2009 - 00:49:19 CDT

Thank You Gustavo, that worked fine for me..

----- Original Message -----
From: Gustavo Seabra <>
To: AMBER Mailing List <>
Sent: Tue, 31 Mar 2009 18:31:41 +0530 (IST)
Subject: Re: [AMBER] problem with the results in the .out file!

On Tue, Mar 31, 2009 at 1:30 AM, Aravind S
<> wrote:
> 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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