Time Step is Incompatible in the NAMD DCD Analyzed with CHARMM

From: twshen (tshen_at_uh.edu)
Date: Wed Jun 18 2008 - 12:28:22 CDT

Hi,

  I did a simulation trajectory for 1 ns with the integration
time step of 2 fs with NAMD 2.6. However, when I tried
 to read the trajectory with CHARMM, it shows that

CHARMM> open unit 51 read unform name "prod01.dcd"
VOPEN> Attempting to open::prod01.dcd::
OPNLGU> Unit 51 opened for READONLY access to prod01.dcd

CHARMM> traj query unit 51

READING TRAJECTORY FROM UNIT 51
NUMBER OF COORDINATE SETS IN FILE: 1000
NUMBER OF PREVIOUS DYNAMICS STEPS: 500
FREQUENCY FOR SAVING COORDINATES: 500
NUMBER OF STEPS FOR CREATION RUN: 500000

NUMBER OF DEGREES OF FREEDOM: 0
NUMBER OF FIXED ATOMS: 0
THE INTEGRATION TIME STEP (PS): 0.0409
THE FILE CONTAINS CRYSTAL UNIT CELL DATA
THE FILE DOES NOT CONTAIN 4-D DATA

The time step is 0.0409 ps recorded in the dcd file, and the
degrees of freedom are not supposed to be zero. Will that
cause a problem when I analyze the trajectory? Thank you
in advance.

Tsaiwei Shen

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