[gmx-users] Re:help!!! "can not fix pbc"

Wei Fu fuwei at adrik.bchs.uh.edu
Mon Feb 23 02:55:01 CET 2004

Hi, David,

    I use GROMACS3.2. I also check energy and temprature, both of them are
OK. I think, maybe the structure is not well optimized, so I use cg
algorithm continue optimize the strucre (set emtol = 300), but this time,
when I heat the protein, it generates the step?.pdb coordinate. How shold
I fix this? 

   In addition, I set pressure with following parameter:
Pcoupl              =  berendsen
tau_p               =  1
compressibility     =  4.5e-5
ref_p               =  1.0

   Since I already optimize the system well, why it still geneartes
step?.pdb file?

Thanks for your help, 



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