Re: Rattle error with lateral pressure calculations

From: Brian Radak (brian.radak_at_gmail.com)
Date: Sat Jul 28 2018 - 12:17:53 CDT

This might just be a wrapping error. Is the DCD generated at constant
pressure? The lattice vectors might not be getting updated via coorfile.

On Tue, Jul 24, 2018, 6:26 PM Sadegh Faramarzi Ganjabad <
safaramarziganjabad_at_mix.wvu.edu> wrote:

> Hello,
>
> 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
> contritbutions
> 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?
>
> Thanks,
> Sadegh Faramarzi,
> Research Assistant
> West Virginia University, Department of Chemistry
> Email:safaramarziganjabad_at_mix.wvu.edu
>

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