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

From: Ross Walker <>
Date: Fri, 19 Oct 2007 09:25:20 -0700

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

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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 - 06:07:50 PDT
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