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-- Svetlana Oard, PhD LSU System Research & Technology c/o 241 La. Emerging Technology Center Baton Rouge, LA 70803 225-270-4499 225-678-5779 On Tue, Aug 21, 2012 at 8:39 PM, case <case.biomaps.rutgers.edu> 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 (nmode.in) and >> for NMODE (nmode2.in) 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 > > > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Thu Aug 23 2012 - 10:00:18 PDT