AMBER Archive (2007)

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

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Oct 18 2007 - 09:53:50 CDT

Hi Samantha,
 
Doing a true restart will not be possible since you don't have the
velocities. 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.
 
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
 
etc.
 
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.
 
Doing things this way minimizes the chances of corruption in mdcrd files. it
also keeps file sizes smaller and more manageable. In addition you have
restart files for every 1ns of your simulation so if anything crashes you
can always go back to the last good restart file. That way you loose at most
1ns of simulation time rather than the whole things.
 
Good luck
Ross
 
/\
\/
|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk <http://www.rosswalker.co.uk/> | PGP Key
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From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
Samantha Kaye
Sent: Thursday, October 18, 2007 06:58
To: amber_at_scripps.edu
Subject: AMBER: Simulation died due to lack of disk space

Unfortunately my simulation (using pmemd) died whilst writing out my rst
file due to lack of disk space. Can someone please advise me on how best to
restart it? I have tried to calculate the number of steps that were
remaining and altered the nstlim param in the .in file accordingly but I
obviously get this error message in my .out file:

ERROR: Could not read coords from trunc_pstat3_mdproduction.rst

I assume I need to generate a new .rst file from my last good frame but
being new to Amber I don't know how or if there is anything I need to be
aware of.

Thanks
Sam 

-- 

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Dr Samantha Kaye

The School of Pharmacy

University of London

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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