[DFTB-Plus-User] Molecules being separated during MD
Ben Hourahine
benjamin.hourahine at strath.ac.uk
Thu Aug 4 20:08:50 CEST 2016
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 <mailto:sharmajncasr at gmail.com>> wrote:
>
>
>
>
>
>
> --------------------------------------------------------------------
> Sharma
> http://www.chem.rochester.edu/groups/huo/people/
> <http://www.chem.rochester.edu/groups/huo/people/>
>
>
> ---------- Forwarded message ----------
> From: *Sharma SRK Chaitanya Yamijala* <sharmajncasr at gmail.com
> <mailto: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
> <mailto: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/
> <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 <mailto: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/
> <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
> <mailto: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/
>> <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
>> <mailto: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/
>> <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
>> <mailto:benjamin.hourahine at strath.ac.uk>> wrote:
>>
>> Hello Sharma,
>>
>> the initial geometry in input.xyz
>> <http://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/
>> <http://www.chem.rochester.edu/groups/huo/people/>
>> >
>> >
>> >
>> > _______________________________________________
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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
>> <tel:%2B44%20141%20548%202325>,
>> benjamin.hourahine at strath.ac.uk
>> <mailto: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
> <tel:%2B44%20141%20548%202325>,
> benjamin.hourahine at strath.ac.uk
> <mailto: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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