Re: AMBER: Simulation died due to lack of disk space

From: Robert Duke <>
Date: Fri, 19 Oct 2007 13:25:21 -0400

>From playing with this sort of thing recently, I vaguely recollect that the step number is appended after a "dot". The last rst is also I believe written both with and without the suffix. This is off the top of my head, so may be off a little, but it is basically pretty easy to work with, aside from the fact that if you get carried away, you will have found another way to fill up a disk, aside from writing out mdcrd too frequently ;-)
Regards - Bob Duke
  ----- Original Message -----
  From: Ross Walker
  Sent: Friday, October 19, 2007 12:25 PM
  Subject: RE: AMBER: Simulation died due to lack of disk space

  Hi Samantha,

  You can just put a minus sign in front of the number of steps specified in ntwr. (See page 91 of the amber 9 manual)

  I.e. ntwr=-10000

  This will get you a unique copy every time. I'm not sure what the naming convention is though and of course it makes automatic scripting difficult since you will have to work out what the rst file will be named. I would still suggest you consider my previous advice:

  For future simulations I would advise splitting things up into chunks. What I normally do is run in 1 to 5ns or so blocks, depending on machine and system size. So something like this:

  Note, mdin is set to restart so irest=1, ntx=5 (restarting from the original heating run)

  pmemd -O -i mdin.1ns -o 0-1ns.out -p prmtop -c heating.rst -r 1ns.rst -x 0-1ns.mdcrd
  gzip -9 0-1ns.mdcrd
  pmemd -O -i mdin.1ns -o 1-2ns.out -p prmtop -c 1ns.rst -r 2ns.rst -x 1-2ns.mdcrd
  gzip -9 1-2ns.mdcrd
  pmemd -O -i mdin.1ns -o 2-3ns.out -p prmtop -c 2ns.rst -r 3ns.rst -x 2-3ns.mdcrd


  You can also put this in a shell script loop if you want - see the last section tutorial 1 on the amber website for an example.

  Since this also minimizes the risk of corrupted trajectory files and also makes file archiving easier.

  All the best
  |\oss Walker

  | HPC Consultant and Staff Scientist |
  | San Diego Supercomputer Center |
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    From: [] On Behalf Of Samantha Kaye
    Sent: Friday, October 19, 2007 02:24
    Subject: Re: AMBER: Simulation died due to lack of disk space

    Thanks Bill, it looks like I'll have to rerun it. Can you tell me, is there a way to stop the restart file overwriting? Perhaps it's possible to dump it out every, say, 1ns.


    Bill Ross wrote:
In theory you could read the mdcrd trajectory file into ptraj
(tell it the frame you want) and then have it write you a restart file. Note
though that this trajectory will not be continuous given the fact that you
will effectively randomize the velocities at this point.
I.e. you will be re-equilibrating.

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Dr Samantha Kaye
The School of Pharmacy
University of London
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Received on Sun Oct 21 2007 - 06:07:51 PDT
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