[gmx-users] Calculation of shape change of a protein during simulation

[Sudip Das]

Dear Joao and Thomas,

Thanks a lot for your kind reply. I am able to calculate the desired
properties by following your answer.

Best regards,
Sudip



‌

Sudip Das

PhD Student
C/o. Prof. S. Balasubramanian
Molecular Simulations Lab
Chemistry and Physics of Materials Unit (CPMU)
Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR)
Bangalore, India

On Wed, Feb 14, 2018 at 10:11 PM, Thomas Evangelidis <tevang3 at gmail.com>
wrote:

> You can calculate properties describing molecular shape using PLUMED as a
> trajectory post-processing tool. Example input:
>
>
> GROUP
> ATOMS=1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,
> 22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,
> 42,43,44,45,46,47
> LABEL=al
>
> GYRATION TYPE=RADIUS ATOMS=al LABEL=rg_al
> GYRATION TYPE=TRACE ATOMS=al LABEL=tr_al
> GYRATION TYPE=GTPC_1 ATOMS=al LABEL=gtpc1_al
> GYRATION TYPE=GTPC_2 ATOMS=al LABEL=gtpc2_al
> GYRATION TYPE=GTPC_3 ATOMS=al LABEL=gtpc3_al
> GYRATION TYPE=ASPHERICITY ATOMS=al LABEL=asph_al
> GYRATION TYPE=ACYLINDRICITY ATOMS=al LABEL=acyl_al
> GYRATION TYPE=KAPPA2 ATOMS=al LABEL=K2_al
> GYRATION TYPE=RGYR_3 ATOMS=al LABEL=g3_al
> GYRATION TYPE=RGYR_2 ATOMS=al LABEL=g2_al
> GYRATION TYPE=RGYR_1 ATOMS=al LABEL=g1_al
>
> PRINT ARG=rg_al,tr_al,gtpc1_al,gtpc2_al,gtpc3_al,asph_al,
> acyl_al,K2_al,g3_al
> ,g2_al,g1_al STRIDE=1 FILE=shape_hsp90
>
>
>
>
>
>
> --
>
> ======================================================================
>
> Dr Thomas Evangelidis
>
> Post-doctoral Researcher
> CEITEC - Central European Institute of Technology
> Masaryk University
> Kamenice 5/A35/2S049,
> 62500 Brno, Czech Republic
>
> email: tevang at pharm.uoa.gr
>
>           tevang3 at gmail.com
>
>
> website: https://sites.google.com/site/thomasevangelidishomepage/
> --
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