AMBER Archive (2009)

Subject: [AMBER] Different simulation times for similar systems

From: Oliver Kuhn (oak.amber_at_web.de)
Date: Mon Dec 14 2009 - 06:31:50 CST

Hi amber users,

I am simulating two HIV protease - inhibitor complex simulations (wildtype and l76v mutant).

I am running the two systems (with equal setups) on our cluster for similar times:

1580 knecht nmwWT_si kuhn R 5-22:44:00 1 node08
1582 knecht nmw76_si kuhn R 5-22:42:00 1 node12

The wt system has already gone to the 5. ns (each production phase is 0.5 ns) while the l76v system is still simulating the second ns.

Preliminary results (timings):

### WT ###
==> wt/min.out <==
| Total time 296.05 (100.0% of ALL )
| Job began at 14:09:47.361 on 12/08/2009
| Setup done at 14:09:49.789 on 12/08/2009
| Run done at 14:14:43.414 on 12/08/2009

==> wt/heat.out <==
| Total time 26210.07 (100.0% of ALL )
| Job began at 14:14:47.666 on 12/08/2009
| Setup done at 14:14:49.719 on 12/08/2009
| Run done at 21:31:37.741 on 12/08/2009

==> wt/prod01.out <==
| Master Total wall time: 53294 seconds 14.80 hours

==> wt/prod02.out <==
| Master Total wall time: 52230 seconds 14.51 hours

==> wt/prod03.out <==
| Master Total wall time: 54318 seconds 15.09 hours

==> wt/prod04.out <==
| Master Total wall time: 49513 seconds 13.75 hours

==> wt/prod05.out <==
| Master Total wall time: 49742 seconds 13.82 hours

==> wt/prod06.out <==
| Master Total wall time: 49788 seconds 13.83 hours

==> wt/prod07.out <==
| Master Total wall time: 49550 seconds 13.76 hours

==> wt/prod08.out <==
| Master Total wall time: 49106 seconds 13.64 hours

==> wt/prod09.out <==
| Master Total wall time: 49093 seconds 13.64 hours

==> wt/prod10.out <==
 NSTEP = 156500 TIME(PS) = 4863.000 TEMP(K) = 299.42 PRESS = -52.4
 ...

### L76V ###
==> l76v/min.out <==
| Total time 214.39 (100.0% of ALL )
| Job began at 14:11:47.965 on 12/08/2009
| Setup done at 14:11:59.925 on 12/08/2009
| Run done at 14:15:22.358 on 12/08/2009

==> l76v/heat.out <==
| Total time 26542.96 (100.0% of ALL )
| Job began at 14:15:29.835 on 12/08/2009
| Setup done at 14:15:31.889 on 12/08/2009
| Run done at 21:37:52.800 on 12/08/2009

==> l76v/prod01.out <==
| Master Total wall time: 54707 seconds 15.20 hours

==> l76v/prod02.out <==
| Master Total wall time: 52301 seconds 14.53 hours

==> l76v/prod03.out <==
| Master Total wall time: 54294 seconds 15.08 hours

==> l76v/prod04.out <==
 NSTEP = 198000 TIME(PS) = 1946.000 TEMP(K) = 298.48 PRESS = 36.5
 ...

How can I check what is causing the slowdown of the l76v simulation and what might be the reason for it!?

Any hint and help is greatly appreciated.

Best regards,
Oliver Kuhn

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