Re: [AMBER] nmode - calculation of vibrational frequencies

From: case <>
Date: Tue, 21 Aug 2012 21:39:40 -0400

On Fri, Aug 17, 2012, Svetlana Oard wrote:

> I am trying to calculate vibrational frequencies using NMODE module. I
> performed a regular minimization and then a Newton-Raphson
> minimization in NMODE to drms = 1.e-6. The later minimization was performed
> successfully with all atoms active. When I try to run nmode , I get the error: “
> "step = 0
> ...
> Root-mean-square gradient of input coords is 3.177878852058610E-005
> This is greater than the requested maximum: 1.000000000000000E-005"
> I attached my nmdin for a Newton-Raphson minimization ( and
> for NMODE ( as well as nmdout files (hcn_nmode.out and
> hcn_nmode2.out). Could you please help me to figure out how to make
> this work?

If I remember correctly, you should use unformatted files as output from the
first step and input to the second, since you are losing just enough precision
in writing formatted output, then reading back in, to avoid the check. You
could also set drms in the second step to 5.E-5.

Better would be to download the current version of AmberTools (there is no
license fee), and use the nmode() function in NAB. It will be faster (no so
crucial here, but would be if you tried bigger systems), you can use the
GB solvent model, and you can minimize and get vibrational modes in a single
step. Remember that Amber8 is more than eight years old (and the nmode
program was written in the early 1980's).

...good luck...dac

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Received on Tue Aug 21 2012 - 19:00:04 PDT
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