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

[Thomas Evangelidis]

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






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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/