[AMBER] Restart Problem: The results of an integrated simulation and restarted simulations are not equal!

From: Ali M. Naserian-Nik <naseriannik.gmail.com>
Date: Mon, 28 Feb 2011 21:26:40 +0330

Hi all,

To find out if splitting a long simulation to some shorter simulations with
the aid of “irest=1” option, I performed two 40 ps test run for a DNA
dodecamer: 1) 40 ps integrated simulation and 2) 20 + 20 ps successive runs
(the 2nd 20 ps simulation was started y restart option “ntx=7” just after
the 1st 20 ps simulation). When I compared the resulting RMSD curves of the
backbone and also PDB files obtained at the end of the two 40 ps
simulations, I found that unexpectedly they are not the same!

Can anyone please guide on this problem?

Whit kind regard,

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Received on Mon Feb 28 2011 - 10:30:04 PST
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