[gmx-users] radius of gyration in REMD of protein

YanhuaOuyang 15901283893 at 163.com
Fri Aug 19 04:28:55 CEST 2016

   I am running a REMD of a protein,  which ranged from 270 to 500K in explicit water model with 60 replicas,  and I stop to analyse the REMD data after running for 50ns. I use the demux.pl script to get the continue the coordinate for each replica. Then I calculate the Rg value for each replica. However, the Rg fluctuation of each replica differs dramatically, some fluctuate dramatically, some converge well. Do someone knows the reason, or the fluctuation is normal ? How can I check my REMD is running correctlly?
the commad of Rg calculation is below:
gmx gyrate -s md_0_0.tpr   -f   *_continue_trajectory_pbc_mol.xtc  -o gyrate_*.xvg

Best regards,

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