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
<amm07bi007_at_students.amrita.ac.in> 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
file.

Gustavo.

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber