Thank you everyone. I managed to do the TICA plots using Pyemma on Google
Colab.
However, I had made the dihedral calculations separately using cpptraj
multihedral command and used that data to make my calculations.
Suchetana
On Wed, Aug 31, 2022 at 10:04 AM Suchetana Gupta <suchetana.gupta.gmail.com>
wrote:
> Thank you Valentin. Ayy idea if Pyemma can be used on Google Colab?
>
> On Wed, Aug 31, 2022 at 5:27 AM Valentin Hörschinger via AMBER <
> amber.ambermd.org> wrote:
>
>> Hi,
>>
>> the excellent PyEMMA Python library (http://www.emma-project.org)
>> supports AMBER trajectories directly as it uses mdtraj internally.
>> There are tutorials available in their documentation of how to produce
>> free energy plots based on tICs.
>>
>> Best regards,
>> Valentin
>>
>> On 8/30/22 20:10, Suchetana Gupta via AMBER wrote:
>>
>> > Hello community
>> > Any help/insights for this?
>> > Thanks
>> > Suchetana
>> >
>> > On Fri, Aug 26, 2022 at 4:08 PM Suchetana Gupta <
>> suchetana.gupta.gmail.com>
>> > wrote:
>> >
>> >> Dear Amber Users
>> >> Is there any way within Amber to get tIC (time lagged independent
>> >> component) plots from our enhanced sampling trajectories? Or any
>> external
>> >> thing where Amber trajectory could be an input for doing these?
>> >>
>> >> Thanks
>> >> Suchetana
>> >>
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>>
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Received on Wed Aug 31 2022 - 12:00:06 PDT
