AMBER Archive (2004)

Subject: RE: AMBER: Question about restart MD

From: Ross Walker (
Date: Mon Oct 11 2004 - 14:06:09 CDT

Dear Xin,
>I was runing a 2ns MD simulations using Amber8. While the job crashed at
about 1.5 ns (around NSTEP=750000),
Do you know why it crashed?
>I restarted the job by using the restart coordinate file and giving a new
file name for -r (md_new.rst) and
>-x (md_new.mdcrd). The job was restarted at about the 1.5ns (not the exact
stop time) but the NSTEP
>started from the begining (NSTEP=100). THe problem is that the job was
still running even the time up
>to 2.5 ns (because of the NSTEP). Should I change the "nstlim=1000000"
before restarting the simulation
>or some other options I should change to control the restart time?
Yes, sander gets the "time" from the restart file but simply uses the file
to obtain the coordinates and velocities. It does not take into account any
other settings, time step, number of steps that have occured etc. Hence you
need to manually adjust the number of steps in your mdin file to ensure that
you stop where you want to. You can work out how many steps are remaining by
checking the time in the top of the restart file and dividing by your time
step. Then just subtract this from the total number of steps you were hoping
to have in the previous run. Note, sander does not write a restrt file on
every step (for performance reasons) but instead writes one every ntwr
steps. Hence the last integer multiple of ntwr steps from the number of
steps actually run will be when the restrt was written.
Although your new job will run for too long, you could always manually
terminate it once it has run as far as you want.
>Is there any way to add the restart output (mdcrd,..) to existing files
while not creating a new one (mdcrd) ?
You can do this by post processing with ptraj. Just give it each of the
mdcrd files, along with the number of frames you want to extract from each
one (necessary if ntwx does not equal ntwr). and then as trajout just give
it a single mdcrd file. You will then get a single mdcrd file containing the
data from each of the input mdcrd files in turn.
>Another question, I mannually terminated the MD job and process the two
trajectory files (initial + restart) using ptraj.
>When I plot the rms, I found there is a big change right at the time of 1.5
ns (from 1.2A remarkedly to 2.5A).
>Is it because of the restart (or restart unproperly)?
This depends... Do other things like the energy etc jump? Also, does this
jump occur only in the restarted file. I.e. Is it due to a failed restrt or
is this jump actually what caused the simulation to crash in the first
place? What was the error message when the first simulation crashed?
Also, when you restarted what options did you specify? Make sure you set
irest=1 and ntx=5 - if you didn't do this then the velocity information will
not have been read from the restart file and so you will have just started
out with new randomised velocities.
Try taking a look at the structures in something like vmd and see if you can
see anything obviously wrong.
All the best

|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- |
| | PGP Key available on request |



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