[DFTB-Plus-User] Molecules being separated during MD

Thu Aug 4 19:27:43 CEST 2016

Dear Ben,

Here is the link for the 28 ps trajectory with only 28 steps (representing
the geometry after each ps). Kindly, have a look. I am not able to send the
xyz file directly to the list as it is > 256 KB (it is 442 KB).

Thanking you,
Sharma.

https://drive.google.com/open?id=0B7l7TJgy0hzhWmxEY1lodEdUdUE

--------------------------------------------------------------------
Sharma
http://www.chem.rochester.edu/groups/huo/people/

On Thu, Aug 4, 2016 at 1:21 PM, Sharma SRK Chaitanya Yamijala <
sharmajncasr at gmail.com> wrote:

>
>
>
>
>
> --------------------------------------------------------------------
> Sharma
> http://www.chem.rochester.edu/groups/huo/people/
>
>
> ---------- Forwarded message ----------
> From: Sharma SRK Chaitanya Yamijala <sharmajncasr at gmail.com>
> Date: Thu, Aug 4, 2016 at 1:18 PM
> Subject: Re: [DFTB-Plus-User] Molecules being separated during MD
> To: User list for DFTB+ related questions <dftb-plus-user at mailman.zfn.
> uni-bremen.de>
>
>
> Hi Ben,
>
> I am confirming that the molecules are moving apart from each other after
> 10 ps (even when the initial geometry is optimized with DFTB+).
>
> Thanking you,
> Sincerely,
> Sharma.
>
> P.S.: I tried to attach images yesterday, but it didn't work. Now, I am
> sending the xyz file with each frame corresponding to the MD geometry after
> each picosecond.
>
>
>
>
>
> --------------------------------------------------------------------
> Sharma
> http://www.chem.rochester.edu/groups/huo/people/
>
>
> On Wed, Aug 3, 2016 at 3:04 PM, Sharma SRK Chaitanya Yamijala <
> sharmajncasr at gmail.com> wrote:
>
>> Dear Ben,
>>
>> Thanks for the reply. When compared to the earlier trajectory (without
>> dftb optimization), the system is not moving apart that much. However, I
>> could see that relative position of both the molecules is changed as given
>> in the attached images (0 and 3ps).
>>
>> At 3 ps, system without dftb optimization also behaved in a similar way,
>> and hence, I expected that the molecules move apart as observed eariler.
>> However, now (after 4ps), I could see that the system is still intact
>> (though polymer has moved from the base of fullerene to the branches of
>> fullerene, which maybe the effect of dynamics and dispersion interactions).
>>
>> In order to check these effects, I am continuing my run (till 30 ps). I
>> will update you.
>>
>> Kindly, let me know whether your observation till 3ps is similar to what
>> I have observed or not.
>>
>> Thanking you,
>> Sincerely,
>> Sharma.
>>
>>
>>
>>
>>
>> --------------------------------------------------------------------
>> Sharma
>> http://www.chem.rochester.edu/groups/huo/people/
>>
>>
>> On Wed, Aug 3, 2016 at 2:07 PM, Ben Hourahine <
>> benjamin.hourahine at strath.ac.uk> wrote:
>>
>>> Hello Sharma,
>>>
>>> after the 30k steps the sulfur containing molecule rotates and move
>>> slightly away for me. The distance from the fullerene increases from 0.34
>>> nm to 0.42 nm, is this the scale of movement you mean?
>>>
>>> Regards
>>>
>>> Ben
>>> On 03/08/16 18:49, Sharma SRK Chaitanya Yamijala wrote:
>>>
>>> Dear Ben,
>>>
>>> After running 3 ps trajectory (after optimizing the initial geometry
>>> with DFTB), I observed similar behavior as mentioned in the earlier e-mails
>>> (molecules moving apart). Could you please confirm whether your calculation
>>> also lead to the similar result or not?
>>>
>>> Thanking you,
>>> Sincerely,
>>> Sharma.
>>>
>>>
>>>
>>>
>>>
>>> --------------------------------------------------------------------
>>> Sharma
>>> http://www.chem.rochester.edu/groups/huo/people/
>>>
>>>
>>> On Mon, Aug 1, 2016 at 6:27 PM, Sharma SRK Chaitanya Yamijala <
>>> sharmajncasr at gmail.com> wrote:
>>>
>>>> Dear Ben,
>>>>
>>>> Thank you for this point and for your time. I will also give a try in
>>>> the way you mentioned.
>>>>
>>>> Thanking you,
>>>> Sincerely,
>>>> Sharma.
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> --------------------------------------------------------------------
>>>> Sharma
>>>> http://www.chem.rochester.edu/groups/huo/people/
>>>>
>>>>
>>>> On Mon, Aug 1, 2016 at 5:01 PM, Ben Hourahine <
>>>> benjamin.hourahine at strath.ac.uk> wrote:
>>>>
>>>>> Hello Sharma,
>>>>>
>>>>> the initial geometry in input.xyz does not seem to have been optimised
>>>>> for the DFTB3 model. So one possibility is that it is the energy stored
>>>>> in the structure coming out during the MD run. I'll start it off from a
>>>>> relaxed geometry and see what happens.
>>>>>
>>>>> Regards
>>>>>
>>>>> Ben
>>>>>
>>>>> On 25/07/16 16:26, Sharma SRK Chaitanya Yamijala wrote:
>>>>> > Dear DFTB members,
>>>>> >
>>>>> > I ran an NVT MD simulation (with Nose-Hover thermostat) of a
>>>>> fullerene and
>>>>> > oligothiophene monomer with a 0.1 fs time step and for a total
>>>>> simulation
>>>>> > time of 30 ps (attached file is for 3 ps). I observed that the
>>>>> molecules
>>>>> > are moving apart from each other after 2 ps or so. Similar
>>>>> simulation with
>>>>> > CP2K didn't show this behavior. Could you please suggest any changes
>>>>> in my
>>>>> > input file to avoid this behavior?
>>>>> >
>>>>> > Thanking you,
>>>>> > Sincerely,
>>>>> > Sharma.
>>>>> >
>>>>> >
>>>>> > --------------------------------------------------------------------
>>>>> > Sharma
>>>>> > http://www.chem.rochester.edu/groups/huo/people/
>>>>> >
>>>>> >
>>>>> >
>>>>> > _______________________________________________
>>>>> > DFTB-Plus-User mailing list
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>>>>> ftb-plus-user
>>>>> >
>>>>>
>>>>> --
>>>>>
>>>>>       Dr. B. Hourahine, SUPA, Department of Physics,
>>>>>     University of Strathclyde, John Anderson Building,
>>>>>             107 Rottenrow, Glasgow G4 0NG, UK.
>>>>>     +44 141 548 2325 <%2B44%20141%20548%202325>,
>>>>> benjamin.hourahine at strath.ac.uk
>>>>>
>>>>> 2013/14 THE Awards Entrepreneurial University of the Year
>>>>>       2012/13 THE Awards UK University of the Year
>>>>>
>>>>>    The University of Strathclyde is a charitable body,
>>>>>         registered in Scotland, number SC015263
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>>> --
>>>       Dr. B. Hourahine, SUPA, Department of Physics,
>>>     University of Strathclyde, John Anderson Building,
>>>             107 Rottenrow, Glasgow G4 0NG, UK.
>>>     +44 141 548 2325, benjamin.hourahine at strath.ac.uk
>>>
>>>
>>> 2013/4 THE Awards Entrepreneurial University of the Year
>>>       2012/13 THE Awards UK University of the Year
>>>
>>>    The University of Strathclyde is a charitable body,
>>>         registered in Scotland, number SC015263
>>>
>>>
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