# AMBER Archive (2006)Subject: AMBER: Question about NSCM

From: Xiaowei (David) Li (xl3a_at_virginia.edu)
Date: Tue Jul 11 2006 - 03:25:48 CDT

Dear amber community:
I am currently trying to calculate the vibrational modes as well as
the absorption spectra in THz frequency range (10-30 cm^-1) of DNA
decamer. My procedure of simulation starts performing 200ps molecular
dynamics of DNA decamer in explicit water with NVE ensemble after
equilibration as described in the AMBER tutorial website. Then the
normal modes of vibration are calcualted using the quasi-harmonic
analysis which is implemented in PTRAJ program. I have found that the
vibrational modes are quite sensitive to the choice of NSCM, which is
the flag for the removing the rotational and translational motions of
COM. The eigenfrequencies between 10-30 cm^-1 for different NSCM are
shown following. The calcualted absorption spectra of DNA are also quite
different in terms of the peak perstions and peak intensities which are
directly related to the eigenvectors. Could anyone give me some hints
how to understand it and make optium choice of NSCM? Thank you very much.

Best,
Xiaowei Li
University of Virginia

NSCM=1: 10.05 10.86 11.39 12.19 12.64 13.17 14.3
14.7 15.21 15.97 16.14 16.88 17.27 18.26 18.55
19.48 20.06 20.55 20.86 21.87 22.43 23.33 23.53
24.15 24.31 25.35 25.95 26.41 27.05 27.83 28.09
28.3 29.18 29.94 30.25;
NSCM=100: 10.56 11.07 11.32 11.87 12.83 12.93 13.3
13.81 14.73 15.31 15.45 15.81 17.16 17.86 18.25
18.84 19.19 19.86 20.65 20.88 21.81 22.06 22.98
23.48 24.16 24.72 25.02 25.95 26.69 26.74 27.3
27.73 28.93 29.25 29.85 30.25 30.44 30.77;
NSCM=1000: 10.15 10.95 11.16 12.13 13.06 13.51
14.28 14.57 15.27 15.29 15.58 16.15 17.02 17.95
18.58 19.08 19.65 19.86 21.08 21.7 22.08 22.55
23.1 23.52 23.93 24.88 25.28 25.9 26.05 26.74
27.65 27.84 28.6 29.16 29.63 30.24 30.59

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