This is the output:
Boundary Condition: orthorhombic
Box matix: 27.3069 0 0
0 27.3069 0
0 0 27.3069
Thanks,
Aditi.
On Wed, Mar 27, 2019 at 4:55 PM Christoph Junghans <[email protected]>
wrote:
>
>
> On Wed, Mar 27, 2019, 14:33 Aditi Khot <[email protected]> wrote:
>
>> I did that using '<box xx="27.3069109148" yy="27.3069109148" zz=
>> "27.3069109148" />'
>> But it still gives this warning 'NOTE: You are using OpenBox boundary
>> conditions. Check if this is intended.'
>>
> I see, can you run your xml file through csg_dump --top and see if the box
> size is reported correctly?
>
> Christoph
>
>
>> Thanks,
>> Aditi.
>>
>> On Wednesday, March 27, 2019 at 3:07:45 PM UTC-4, Christoph Junghans
>> wrote:
>>>
>>>
>>>
>>> On Wed, Mar 27, 2019 at 13:53 Aditi Khot <[email protected]> wrote:
>>>
>>>> Hi Christoph,
>>>>
>>>> Thanks for the reply. I had another question. If I am have an atomistic
>>>> trajectory file with periodic boundary conditions, do I need to unwrap the
>>>> coordinates before supplying it to VOTCA? I could not find an option to
>>>> specify boundary conditions.
>>>>
>>> There is an option in the xml topology to set the box size. If you do
>>> that periodical boundaries are assumed and minimum image convention is
>>> applied. Otherwise open boundaries are used.
>>>
>>> Christoph
>>>
>>>>
>>>>
>>>> Thanks,
>>>> Aditi.
>>>>
>>>> On Tuesday, March 26, 2019 at 8:15:11 PM UTC-4, Christoph Junghans
>>>> wrote:
>>>>>
>>>>>
>>>>>
>>>>> On Tue, Mar 26, 2019, 17:49 Aditi Khot <[email protected]> wrote:
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> I want to perform force matching using VOTCA. My group uses LAMMPS
>>>>>> for MD simulations. So, I am generating a '.h5' file to supply as a
>>>>>> trajectory file to VOTCA. I do not have '.tpr' file for topology, so I am
>>>>>> defining the atomistic topology in an xml file according to Pg. 14 in
>>>>>> VOTCA
>>>>>> manual.
>>>>>>
>>>>>> I wanted to reconfirm if this will work. And should I supply the
>>>>>> topology xml file as argument to '--top' option? Please clarify these
>>>>>> doubts.
>>>>>>
>>>>> Yes, that should be fine, you can combine pretty much all topology
>>>>> files with all trajectory files.
>>>>>
>>>>> Christoph
>>>>>
>>>>>>
>>>>>> Thanks in advance!
>>>>>>
>>>>>> Aditi.
>>>>>>
>>>>>>
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>>>>>
>>>>>
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>>>>>>
>>>>> --
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>>> --
>>> Christoph Junghans
>>> Web: http://www.compphys.de
>>>
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--
Aditi Khot,
Dual Degree Final Year,
Chemical Engineering,
Indian Institute of Technology, Madras.
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