On Thu, Jan 28, 2010, xueqin pang wrote:
>
> I am trying to work with nmode now and wanna to know why the
> default value for DIELC is 4?
It's not: the default value is 1.0; see line 52 of rdinp.f
> Secondly, I want to do a minimisation before nmode and try to
> keep that confirmation during nmode minimisation. In this case what
> is the biggest DRMS to use. And do I have to use the input values in
> nmode-minimisation as well as strip all the water molecular?
I don't understand the question. Nmode will take whatever conformation you
give it in the input file; typically, this would have been minimized in
sander, but that is up to you. You can use nmode to both minimize and to
compute normal modes if you wish...that is often easier.
[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.]
...dac
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Received on Thu Jan 28 2010 - 05:30:04 PST
