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

Ben Hourahine benjamin.hourahine at strath.ac.uk
Wed Aug 3 20:07:32 CEST 2016


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 <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/
>
>
>     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/
>         >
>         >
>         >
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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
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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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