[AMBER] Fwd: About long simulation

From: haris p <hariskalikav.gmail.com>
Date: Wed, 16 Feb 2011 21:17:19 +0530

---------- Forwarded message ----------
From: haris p <hariskalikav.gmail.com>
Date: Wed, Feb 16, 2011 at 4:12 PM
Subject: About long simulation
To: modesto.mmb.pcb.ub.es


 I am a research scholar working on molecular dynamics simulation studies on
nucleic acids. During the production run, at about ~23rd ns our work crashed
and it was found that the coordinates of water over flowed the limit and
"rst" file contains ********* error. We have tried " iwrap = 1 " from the
first production run itself. But after two steps ( 200ps each) our DNA split
apart in to two strands. Still the work continues and in the next step the
strand recombine and proceeds. Na+ ions were also moved apart. We were
running two works, both with " iwrap = 1 ", both works show the same problem
in the same step. It would be very helpful if you could give us some idea on
the technique you applied on the long simulation using AMBER.

Thanking You in anticipation,

Research Scholar
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Received on Wed Feb 16 2011 - 08:00:05 PST
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