[gmx-users] Distorted protein structure after MD simulation

Mark Abraham Mark.Abraham at anu.edu.au
Wed Mar 31 09:54:46 CEST 2010

On 31/03/2010 5:48 PM, sonali dhindwal wrote:
> 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 ?

There are many possible reasons, chief among them an inappropriate model 
physics. With no idea what your metal ion is, how you've built your 
topology and what ensemble you've used, we can't have any better ideas 
for you. :-)


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