Case,
Thanks for your reply.
"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.
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?
I am quite outside of this field and sorry for these naive questions
Thanks again for you help
Xueqin
--- 10年1月28日，周四, case <case.biomaps.rutgers.edu> 写道：
发件人: case <case.biomaps.rutgers.edu>
主题: Re: [AMBER] questions with nmode
收件人: "AMBER Mailing List" <amber.ambermd.org>
日期: 2010年1月28日,周四,下午9:21
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 - 20:00:03 PST
