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

Thu Aug 4 19:21:14 CEST 2016

--------------------------------------------------------------------
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
>>>> > DFTB-Plus-User at mailman.zfn.uni-bremen.de
>>>> > https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/
>>>> dftb-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
>>>> _______________________________________________
>>>> DFTB-Plus-User mailing list
>>>> DFTB-Plus-User at mailman.zfn.uni-bremen.de
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>>>> dftb-plus-user
>>>
>>>
>>>
>>
>>
>> _______________________________________________
>> DFTB-Plus-User mailing listDFTB-Plus-User at mailman.zfn.uni-bremen.dehttps://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-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, 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
>>
>>
>> _______________________________________________
>> DFTB-Plus-User mailing list
>> DFTB-Plus-User at mailman.zfn.uni-bremen.de
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>
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