Re: Using PBC tools for a cubic and a rectangular box

From: Brian Radak (brian.radak_at_gmail.com)
Date: Tue Mar 27 2018 - 09:03:55 CDT

Oh, was my explanation incorrect? I might also be mis-remembering from
experience with AMBER NetCDF rather than DCD files.

On Tue, Mar 27, 2018 at 9:35 AM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:

>
>
> On Tue, Mar 27, 2018 at 9:09 AM, Brian Radak <brian.radak_at_gmail.com>
> wrote:
>
>> Hi Monika,
>>
>> The usage of pbctools is a little more complicated than what you are
>> doing. I recommend looking at the plugin documentation (
>> https://www-s.ks.uiuc.edu/Research/vmd/plugins/pbctools/)
>>
>> Short explanation - pbctools does not know anything about your box
>> dimensions (which MUST be orthorhombic) until you tell it. That information
>> is NOT extracted from the DCD frames, but can be read from an XST
>> trajectory.
>>
>
> I'm not sure that's the problem... "pbc get -all" may tell whether the
> correct unit cell is being read for each DCD frame.
>
> Monika, I would definitely try to visualize the trajectory in VMD after
> wrapping.
>
> At times I found pbc unwrap to give incorrect results (i.e. a few waters
> had bonds longer than one unit cell). In those cases, qunwrap gave correct
> results, and was also much faster:
> https://github.com/jhenin/qwrap
> If the system topology is set in a way that VMD sees each molecule as a
> distinct "fragment", I would recommend:
> qunwrap compound fragment
>
> This worked well for me for polymer simulations in LAMMPS, which unlike
> NAMD wraps every single atoms in the original unit cell (i.e. breaking
> bonds).
>
> Giacomo
>
>
>
>>
>> This will assign your fixed box size to all frames, *then* you can
>> unwrap.
>> % pbc set cell {30.0 30.0 30.0} -all
>>
>> HTH,
>> BKR
>>
>>
>> On Tue, Mar 27, 2018 at 6:34 AM, Monika Madhavi <monikamadhavi_at_gmail.com>
>> wrote:
>>
>>> Dear all,
>>>
>>> I did a water simulation in a cubic box (30x30x30) Å and in a
>>> rectangular box (60x60x120) and I calculated the same property of water
>>> (spin relaxation rate constants). However, the two results I get are
>>> different to each other. I suspect this could be a problem with PBC.
>>>
>>> In each simulation, I used cellBasisVectors as the length of each side
>>> of the box. i.e.
>>> 30 0 0
>>> 0 30 0
>>> 0 0 30
>>>
>>> and
>>> 60 0 0
>>> 0 60 0
>>> 0 0 120
>>>
>>> and when analyzing the trajectory using a tcl script in vmd, I used the
>>> following command to unwrap the system
>>> package require pbctools
>>> pbc unwrap -molid $mol -all
>>>
>>> But the result is the same as before.
>>>
>>> I am not very confident about how pbc works in namd and how to unwrap
>>> the trajectory properly. I would like to know whether the way I unwrapped
>>> the trajectory is correct and some insight for the reasons to get this kind
>>> of a result.
>>>
>>> Thank you.
>>> Best regards,
>>> Monika
>>>
>>> --
>>> W.A.Monika Madhavi
>>> Lecturer (Probation),
>>> Department of Physics,
>>> University of Colombo.
>>>
>>
>>
>
>
> --
> Giacomo Fiorin
> Associate Professor of Research, Temple University, Philadelphia, PA
> Contractor, National Institutes of Health, Bethesda, MD
> http://goo.gl/Q3TBQU
> https://github.com/giacomofiorin
>

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