[gmx-users] molecules blowing up

[Yegor Isakov]

I appreciate if  anybody could answer my question?
 ,
       My molecules continue blowing out. I have got a peptide where a  carbonyl group is connected to cysteine through S atom (-S-CO-). I inserted my topology (the whole set including peptide.top, peptide.gro, and posre.itp ) into gmxdemo script (water) and run it the same way as the demo cpeptide. My molecule blows out at the third step of the run.  In the program output I have got a message that the force is concentrated on the S atom. 
        I have got another molecule where carbonyl group was attached to protein through NH group (-NH-CO-). This bond is stable enough and the molecule runs fine up to 3000 steps.
 Thus, I concluded that the problem is that (-S-CO-) bond. Actually I did not find  this bond in the libraries and I introduced it myself into my topology by just adding the the physical length of the bond. I believe that's not enough. 
      My question is: what I need to do to introduce into my MD model a new bond that was not previously described in those libraries? The manual does not cover this topic explicitly. 
 Thank you in advance.
 Faithfully,
 Yegor
     

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