Re: Rattle error with lateral pressure calculations

From: Brian Radak (brian.radak_at_gmail.com)
Date: Mon Jul 30 2018 - 08:29:44 CDT

If you have dynamics output - do the energies (I would check POTENTIAL
and/or ELECT) match when just using a simple coorfile script?

On Sun, Jul 29, 2018 at 11:18 PM, Sadegh Faramarzi Ganjabad <
safaramarziganjabad_at_mix.wvu.edu> wrote:

> 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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