AMBER Archive (2009)

Subject: RE: [AMBER] Restarting an MD Simulation

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed Feb 04 2009 - 21:03:36 CST

Hi Robert,

To be honest I didn't even know this option existed and I'm not surprised
that it doesn't work. When I get back online I'll try this myself and see if
I can reproduce it. One thing to note though is that there is nothing
actually wrong with your restarted MD run except that the value of nstep got
reset. Everything else including the Time should continue as if it were
restarted. Hence if you were to plot things against the time in the output
file it should be continuous. Also reading in the two trajectories into
ptraj for example, one after the other, should give you the same results as
if it were a single run.

It would probably be possible to devise some kind of awk script that would
go through and add 179000 to every nstep value in your output file which
would give you what you were expecting I guess.

All the best
Ross

> -----Original Message-----
> From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
> Behalf Of Hopkins, Robert
> Sent: Wednesday, February 04, 2009 4:34 PM
> To: AMBER_at_ambermd.org
> Subject: [AMBER] Restarting an MD Simulation
>
> Amber Users,
>
>
>
> I'm using AMBER9 to do some MD calculations and one of my runs was
> stopped after NSTEP = 179000 because of a power glitch. The restart
> file at this point was named IIL.rst. After reading about Weight
> Change Information for NSTEP0 on p. 109 of the User's Manual, it
> appeared that restarting the run with NSTEP=180000 and continuing to
> NSTEP=250000 should be straightforward. So, I used the following mdin
> file:
>
>
>
> Continue dodecamer equilibration at 300K & P=const.; no DNA restraints;
>
> SHAKE on; MD on; from NSTEP 180000 to 250000.
>
> &cntrl
>
> imin = 0, irest = 1, ntx = 5,
>
> nstlim = 71000, dt = 0.002,
>
> ntc = 2, ntf = 2,
>
> cut = 8.0, ntb = 2, ntp = 1, taup = 2.0,
>
> ntpr = 1000, ntwx = 1000,
>
> ntt = 3, gamma_ln = 2.0,
>
> temp0 = 300.0, nmropt =1
>
> /
>
> &wt type='NSTEP0', istep1=179000 /
>
> &wt type='END' /
>
>
>
> along with the command:
>
>
>
> sander -O -i mdin -o IIL2.out -p IIL_sol.prmtop -c IIL.rst -r
> IIL2.rst -x IIL2.mdcrd &
>
>
>
> The MD calculation evidently proceeded as expected except that the
> values of NSTEP began at 1000 and continued to 71000. I'd appreciate
> any suggestions of what I need to do differently to correct this result.
> Thanks.
>
>
>
> Bob Hopkins
>
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