Re: Rattle error with lateral pressure calculations

From: Sadegh Faramarzi Ganjabad (safaramarziganjabad_at_mix.wvu.edu)
Date: Thu Aug 02 2018 - 13:28:52 CDT

Brian,

Unfortunately, I don't have xst files. I ran a short version of the
simulation at constant volume and did the lateral pressure calculation. It
works fine now. I think your interpretation is right.

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

On Tue, Jul 31, 2018 at 1:41 PM, Brian Radak <brian.radak_at_gmail.com> wrote:

> If the energies from stdout and post-processing frames do not match to at
> least 3 decimals then I would say that you probably can't trust the results
> and something is wrong.
>
> My suspicion is that coorfile does not cause the cell basis vectors to be
> updated at each frame, even though that information should be present in
> the dcd file. You might have to extract this by some other means (did you
> write an xst file by chance?) and then manually reset cellBasisVector1/2/3
> inside your while statement.
>
> I've never actually used the pressureProfile code before, so I have no
> idea how it is supposed to be used in practice. Does the simulation have to
> be constant pressure? Constant volume could solve the problem. You might
> consider running a short NVT simulation and then repeating your analysis
> procedure. If that solves the problem then I'm probably correct, if not,
> then it must be something else entirely.
>
> HTH,
> BKR
>
> On Tue, Jul 31, 2018 at 1:11 PM, Sadegh Faramarzi Ganjabad <
> safaramarziganjabad_at_mix.wvu.edu> wrote:
>
>> Brian,
>>
>> I get the error right after the energies appear on the output for the
>> first time. The ELECT energy is %30 different from the original trajectory.
>>
>> Sadegh Faramarzi,
>> Research Assistant
>> West Virginia University, Department of Chemistry
>> Email:safaramarziganjabad_at_mix.wvu.edu
>>
>> On Mon, Jul 30, 2018 at 9:29 AM, Brian Radak <brian.radak_at_gmail.com>
>> wrote:
>>
>>> 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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