AMBER Archive (2009)

Subject: [AMBER] ERROR: Could not read coords from {filename}

From: Paul Brandt (brandt.j_at_gene.com)
Date: Sun Dec 27 2009 - 22:14:50 CST

Dear Amber Users and Developers,

 

I cannot restart a simulation using the final rst file. I am running
several simulations with the same input control variables (see below). Each
simulation is identical except for the seed number used for the
randomization of initial velocities. After ~42 nsec of simulation (~320k
atoms), broken up into 200 psec chunks, one of the simulations won't restart
from the final rst file. The others are running fine. If I save an
intermittent rst file for this particular simulation, the next chunk of
trajectory will restart, but when I try to start a new 200 psec chunk with
the final rst file I find the following message in the next chunk's output
file: ERROR: Could not read coords from {filename}

 

Everything is exactly the same as the other simulations. I used sed to
systematically replace filenames in my input scripts, so I am sure there are
no typographical errors present (otherwise other simulations would have had
the same error).

 

Below are the control variables I use:

 

scee=1.2,

        ntx=7,

        ntb=2,

        nstlim=100000,

        ntwe=50,

        ntpr=1000,

        nsnb=10,

        irest=0,

        imin=0,

        ntt=1,

        npscal=1,

        temp0=300,

        dt=0.002,

        ntp=1,

        ntc=2,

        pres0=1,

        tempi=300,

        ntwx=1000,

        ntf=2,

        cut=9

 &end

 

Any idea why this is happening?

 

Thanks a lot!

 

 

Paul

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