[gmx-users] Distorted protein structure after MD simulation

sonali dhindwal sonali11dhindwal at yahoo.co.in
Wed Mar 31 08:48:11 CEST 2010

Hello All,
I have done one MD similation for 1 ns for my protein, having two ligands and one metal ion with GROMOS96 43a1 force field and  dodecahedron box as tge unit cell.
After simulation when i checked RMSD, it is increasing till 1ns and observing the .gro file in VMD, I have seen that, my protein structre is very much distorted,  intialy it had tim barell topolgy with 8 beeta sheets and 8 alpha sheets,,now only 7 sheets are remaing,one became coiled strucutre. What could b the possible reason ? 
Thanks in advance.

Sonali Dhindwal

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