Re: [AMBER] Restart file for pmemd not showing all information

From: Ross Walker <>
Date: Thu, 22 Dec 2011 09:10:24 -0800

Hi Sasha,

I suspect this is a buffering issue with the file system. Have you tried
killing a job mid cycle and seeing if the restart file then gets the rest of
the information written to it?

What is happening is that your operating system is buffering the information
being written to the restart file. As far as pmemd is concerned everything
got written correctly and indeed if it were to close and reopen the restart
file it would be able to read all the information. Also if your job crashes,
since it is the operating system that is buffering it so the remaining
restart file information should get flushed. Your best option is to try
killing a job 'kill -9 PID' and see what happens to the restart file that is

If it is still not writing it then we can take a look and see what else
might be causing it.

All the best

> -----Original Message-----
> From: Sasha Perkins []
> Sent: Thursday, December 22, 2011 8:48 AM
> To:
> Subject: [AMBER] Restart file for pmemd not showing all information
> Hello,
> This is one of my steps in my simulation. I noticed, however, that each
> time the restart file is written during my run, there are about 80
> atoms
> (my system has a total of 9600 atoms) who's information is not written
> in
> the restart file, as well as the box information is missing. However,
> at
> the end of the run, all information is written for the last cycle.
> Prior
> runs with the same input file but using sander showed all information
> in
> the restart files every time the file was written.
> Below is my input file which I am running using pmemd in amber 11.
> &cntrl
> imin = 0, irest=1, ntx=5,
> ntb=2, ntp=1, taup=1.0,
> pres0=0.98,
> cut = 20.0,
> ntc=2, ntf=2,
> temp0=298.0,
> ntt=3, gamma_ln=5,
> nstlim= 400000, dt =0.002,
> ntpr=100, ntwx= 100, ntwr = 1000
> &end
> Any helpful information regarding how to fix this, or if this is
> normal,
> would be greatly appreciated since I need all information to be written
> in
> the restart files in case my runs unexpectedly get terminated before
> the
> maximum number of cycles is reached.
> Thank you,
> Sasha Perkins
> Graduate Student, Penn State University
> _______________________________________________
> AMBER mailing list

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Received on Thu Dec 22 2011 - 09:30:03 PST
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