Re: AMBER: Controlling number of water residues...

From: David A. Case <>
Date: Tue, 1 Mar 2005 08:25:14 -0800

On Mon, Feb 28, 2005, Pavan G wrote:

> However, the
> system was fine till minimization was over but on running MD (sander),
> it gave no output, both the .out and .mdcrd files were empty. I
> suspect that large empty (vaccum) spaces around the boxes might have
> led to instabilities.

You are right to be leery of having large empty spaces, but "instabilities"
should not lead to empty output files. Sander prints a lot of information
before even starting to do any calculations. So you will need to search
for why your output files are empty. Start from the inputs that worked for
minimization, and try to modify them in a minimal way, running (say) just
10 steps of dynamics with ntpr=1.

....good luck....dac

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Received on Tue Mar 01 2005 - 16:53:00 PST
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