[gmx-users] splitting of chains

özge kül ozgekul8233 at yahoo.com
Fri Mar 30 15:31:44 CEST 2007

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

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