On Fri, Jan 29, 2010, xueqin pang wrote:
>
> "You can use nmode to both minimise and to compute normal modes if you wish..."
> how to choose it? I tried to set maxcyc=100, but nmode stopped calculation.
You will need to either study the source code, and/or get the Amber 9 Users'
Manual from the Amber web site, and look at the nmode section there.
>
> If I want nmode to do normal mode calculations only, should the previous
> conformation minimisation be done in vacuum, and how to make sure the
> confirmation is good enough for normal mode calculations?
This depends somewhat on the size of your system. People report that
gradients around 10**-5 kcal/mol-A are generally good enough; I personally
don't like to have to worry about this aspect, and simply minimize everything
to below 10**-9 rms gradient.
>
> [Aside: if you are going to spend time learning a new program anyway, running
> normal mode calculations in NAB might be a better way to proceed. See the
> AmberTools Users' Manual, plus $AMBEHROME/test/nab/asp.nab for a sample
> program.]
At the risk of beating a dead horse, I have re-posted my earlier comments
above.
...dac
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Received on Fri Jan 29 2010 - 09:30:02 PST
