[gmx-users] splitting of chains

[özge kül]

After making Md simulation and getting the rmsd,gyration.. analyzing graphics I looked at the VMD.Then I saw  that the 2 chains are getting splitting at a time.And then got together.So I could understand why the graphics are so bad.Then I read the manual.It says I should use -merge in pdb2gmx line if you have disulphite bridges.My molecule has 2 chains that has disulfite bonds..Anything else that you know about this except -merge?
   
  Thank you
  özge

 
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