Rattle error with lateral pressure calculations

From: Sadegh Faramarzi Ganjabad (safaramarziganjabad_at_mix.wvu.edu)
Date: Tue Jul 24 2018 - 17:24:17 CDT


I am doing lateral pressure calculations on a dcd trajectory. Here is the
section for pressure profile calculation on NAMD configuration;

# set pressure profile parameters
pressureProfile on # on to record kinetic, bonded and nb
pressureProfileSlabs 80 # number of slabs along z
pressureProfileFreq 10 # output frequency in timesteps
pressureProfileEwald on # when on only Ewald contribution is computed
pressureProfileEwaldX 75 # number of vectors along x
pressureProfileEwaldY 75 # number of vectors along y
pressureProfileEwaldZ 96 # number of vectors along z

set ts 0
firstTimestep $ts

# run pressure calculation
coorfile open dcd 1-2Stride100WrappedAligned.dcd
while { [coorfile read] != -1 } {
  incr ts 1000
  firstTimestep $ts
  run 0
coorfile close

The rest of parameters in the configuration file are pretty much the same
as my original MD simulations, except I deleted the minimization and run
section. I keep getting rattle error after a couple of timesteps. I thought
with this setup I just use the already existing dcd file, rather than
running a new simulation that might crash. I'm not sure how to get rid of
this error. Do I have to modify my trajectory prior to the calculation?

Sadegh Faramarzi,
Research Assistant
West Virginia University, Department of Chemistry

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