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

[Sharma SRK Chaitanya Yamijala]

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/
>> >
>> >
>> >
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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
>>
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>>
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