Re: [AMBER] nmode - calculation of vibrational frequencies

From: Svetlana Oard <>
Date: Thu, 23 Aug 2012 11:53:09 -0500

Dear Dr. Case,
Thank you very much for the answer. I will try both ways.
Svetlana Oard, PhD
LSU System Research & Technology
c/o 241 La. Emerging Technology Center
Baton Rouge, LA 70803
On Tue, Aug 21, 2012 at 8:39 PM, case <> wrote:
> 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 Thu Aug 23 2012 - 10:00:18 PDT
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