[DFTB-Plus-User] Molecules being separated during MD
Sharma SRK Chaitanya Yamijala
sharmajncasr at gmail.com
Mon Aug 15 23:13:27 CEST 2016
Dear Ben,
I have checked the trajectory with dispersion interactions (lj with UFF
parameters in DFTB) and* it worked *(molecules are not separating anymore
after 30 ps also).
Thanks a lot for your help,
Sincerely,
Sharma.
--------------------------------------------------------------------
Sharma
http://www.chem.rochester.edu/groups/huo/people/
On Thu, Aug 4, 2016 at 2:08 PM, Ben Hourahine <
benjamin.hourahine at strath.ac.uk> wrote:
> Hello Sharma,
>
> we should probably move the discussion off list, but is this system
> perhaps bound together by dispersion interactions in the CP2K model you
> used? These are turned off for the dftb_in.hsd.
> Regards
>
> Ben
>
>
> On 04/08/16 18:27, Sharma SRK Chaitanya Yamijala wrote:
>
> 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.un
>> i-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/d
>>>>>> 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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>>>>>> ftb-plus-user
>>>>>
>>>>>
>>>>>
>>>>
>>>>
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>>>> 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
>>>>
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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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