Re: Rattle error with lateral pressure calculations

From: Sadegh Faramarzi Ganjabad (safaramarziganjabad_at_mix.wvu.edu)
Date: Sun Jul 29 2018 - 22:18:39 CDT

Brian,

Thanks for replying. Yes, the DCD is generated at constant pressure. The
trajectory is wrapped. Is there a way to check if lattice vectors are
updated?

Best,
Sadegh Faramarzi,
Research Assistant
West Virginia University, Department of Chemistry
Email:safaramarziganjabad_at_mix.wvu.edu

On Sat, Jul 28, 2018 at 1:17 PM, Brian Radak <brian.radak_at_gmail.com> wrote:

> 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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